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Cyborg 009: The original ending of the manga and 2001 anime qualifies as a bittersweet ending. After the final battle in space, Black Ghost is finally destroyed and 009/Joe seemingly falls to his death, only to be saved by 002/Jet, but then 002 runs out of fuel and the two friends fall to their death through the Earth's atmosphere, appearing as a shooting star.
Gunbuster: Perhaps the first example for many '90s Anime fans, the end of the sixth OVA episode in which Noriko and Kazumi within Gun Buster One had to enter Gun Buster Three in order to detonate the bomb within. Due to time dilation effect, they returns home with 10,000 years having passed on Earth. A joyous reunion with human civilization alive well with a spectacular welcome long prepared for them, but without their peers, who have long since died.
The sequel Diebuster kills off Nono by saving the entire universe from collapsing from an errant black hole after killing off the last remaining space monster.
Also the manga sequel "Aim for the Top! The Next Generation" had their friend Jung Frued live on for quite some time due to suspended animation/light speed travel... never got to finish it so not sure if she's actually alive when the Gunbuster gets back... she was looking for it though.
The ending to the third season of the Slayers anime (Slayers TRY) had the world saved once again...at the cost of the welfare of both a twisted yet hurt survivor of a mass slaughter and an entire other planet. It may as well be that Sirius is the only living denizen of the Overworld left. The four protagonists feel rather unsatisfied and bittersweet about the outcome.
The ending to season 5 (Evolution-R) is far more satisfying, but there's a bittersweet regard involving Pokota, who will more or less spend the rest of his life stuck as an unaging stuffed animal due to his posessed human body being destroyed out of necessity.
And the final novel of the main series ends triumphantly for Lina and Gourry as they decide to visit Lina's home kingdom. The cost of this was killing off the mentally conflicted Luke, who had transformed into Shabranigdo; this happened to him because the woman he loved, Milina, was poisoned, denied medical treatment, and died.
Devilman Lady: Jun defeats the Child of God at the expense of the lives of all of her friends, including her love interest Kazumi, whose gruesome death as she was absorbed into Jun she was forced to watch; and she lost both her arms. However, the last scene is a human child playing with a Devil Beast child, suggesting that humanity is accepting their successors without any more violence.
Princess Tutu: The story is done, the good guys win, Rue and Mytho show their true love and this lets them defeat the Raven with the help of Tutu and Fakir... but not only do Rue and Mytho have to leave Kinkan Town so he can reclaim his throne, but Ahiru/Tutu has to return to her original duck form forever. The final shot of the series shows Fakir relaxedly fishing in a pond, while Ahiru happily swims nearby his feet, implying that they stayed together, but with Fakir owning Ahiru as his pet.
Simoun. All the Sibyllae have made their choices. Neviril, Aaeru, Dominura, Limone, and Yun stay "young" forever, with the strange consequences that entails. Everyone else takes the plunge and grows up. Time passes, people change, war comes and goes... and life, as it always does, goes on.
The ending of Wolf's Rain features the protagonists finally making their way to their destination of Paradise only to be systematically killed one by one by the now deranged Big Bad, Lord Darcia. After he's finally killed, only Kiba, and Cheza, the girl he was trying to protect, remain, both of whom are slowly dying as well. She proceeds to attempt to use her powers to recreate Paradise, only for the world to be corrupted by the presence of Darcia's severed eyeball. We are then treated to an ambiguous Distant Finale where we see the wolves have apparently been reincarnated in our modern world, when we suddenly cut to black. Seen by some as an outright Shoot the Shaggy Dog ending.
Tengen Toppa Gurren Lagann was arguably not this kind of ending, with characters going out in blazes of glory that fit their characters and the series' over-the-top style... until Nia died after the final battle (on her wedding day, no less) as a result of her Anti-Spiral nature being tied to the destruction of the Anti-Spiral himself in the previous episode. Fan division over this is rampant regarding whether Simon's calm acceptance of her death before his eyes is him refusing to make Lord Genome's mistake by attempting to play God or undermining the show's premise of changing Fate itself by pure refusal to accept it and overriding willpower.
FLCL, in both anime and manga formats, probably fits here as well. Naota matures a good deal and doesn't let the world or his friends be glassed, but it certainly isn't the happiest ending.
At least Haruko offers Naota to come with her "the next time", whatever that means. We can has sequel, please?
Even more bittersweet is the ending for Char's Counterattack, in which Axis is reversed and Earth is saved, but Amuro and Char die in the process.
Gundam F91 does the opposite of this with the hero managing to save his love interest and keep all his friends alive, but his side winds up losing the actual war and their home town is conquered. Gundam doesn't do happy endings.
Gundam 0080: War In The Pocket seems to be considered an exemplar of this, the colony is saved from nuking and Al and Chris survive the whole affair, but Bernie dies needlessly, Al is forever traumatized and Chris is in the dark about the fact that she killed her lover.
Gundam Wing seemed to be a rarity in that really no loved ones were harmed in the making of this show and everything works out perfectly. Everybody that dies is either a mook, a one-episode character, straight villains, or Treize Kushrenada. Even the big bad, Zechs, manages to survive the finale... somehow.
Gundam Seed the protagonists manage to prevent ZAFT and the Earth Alliance from completing obliterating each other (and the rest of humanity), but most of the cast is dead and there is no decisive end to the war or Natural/Coordinator resentment, allowing for another, even more brutal war to follow only two years later.
The Gaara Retrieval Arc of Naruto ended on a rather bittersweet note, since the team saves Gaara, but Elder Chiyo dies in the process to revive him.
Similarly, the Land of Waves arc; the bridge is completed, hope is restored, and Gato is dead and no longer able to oppress the people, but Haku and Zabuza's deaths deeply impact Team 7 and make them question what it means to be a ninja. The Invasion of Konoha Arc ends with the village saved from destruction at Orochimaru's hands, but the Third Hokage and many other ninja die in the process.
Kurau in Kurau Phantom Memory manages to save the world from the in-pouring Rynax, but loses her own Rynax in the fight, which causes her pair Christmas many years of bitter loneliness. Luckily, Christmas' pair returns in the Distant Finale, but of course she is not quite the same one as before. The human Kurau also has good memories of her time she was filled with her Rynax, but arguably changes into a much less colorful person than she was back then.
The first Fist of the North Star series ends with Kenshiro finally defeating Raoh... and then discovering that Yuria is dying from radiation sickness. We find out in the second series that she lived on for a couple of years before telling Kenshiro to continue living without her.
The graduation episode of Azumanga Daioh. Saying goodbye is never easy.
There's a particularly bittersweet bit near the end: a scene (or panel, if you're reading the manga) of all six girls bowing respectfully to Yukari, with the words "Thank you very much." appearing above them. They do this facing "out", so it has the effect of actors taking a curtain call.
Similarly, the ending of Lucky Star is quite melancholic despite (or perhaps even because of) all the girls performing the whole theme song in cheerleading outfits.
The penultimate episode also fits this trope: We learn that Mama Kanata's ghost is still watching over Konata and Sojiro, but they are completely unaware of her presence, and upon finding proof of her existence, misinterpret it as evidence that they are being haunted by an unfriendly ghost and burn it.
Not to mention that the group has finished school and will presumably go to different colleges.
In One Piece, the entire Whitebeard War Saga (Thriller Bark arc, Sabaody Archipelago arc, Amazon Lily arc, Impel Down arc and Marineford arc together) is as big an example of this as you're gonna get in this series. Preparing for the New World, the Straw Hat Pirates meet up with new friends, an old enemy-since-reformed, new enemies reforming, and icons of the old age of Piracy. What follows later (in chronological order) is: They encounter the cruelty of the world's nobles after one of their friends are kidnapped and the other shot; they face up against three adversaries which alone are much too powerful for them leading to the crew is forcibly split up; Luffy finds out his brother is being held at the world's worst prison awaiting public execution, and after entire said prison, gets his ass handed to him so soundly he had to give ten years of his life to keep going, and after failing to spring his brother, loses one of his friends just so he and many of his newfound allies can escape; Quickly made apparent he is nowhere near strong enough to hold his own against the Marines' elite soldiers, and even when it looks like he's saved Ace Admiral Akainu ruthlessly kills him right in front of Luffy, to bring the point home, leading to Luffy finally mentally collapsing. It's bittersweet because at least Luffy survived, his crew is okay albeit separated, and after they become stronger they can reunite to enter the New World together.
As for global ramifications, Ace as mentioned before died, ending the bloodline of Gold Roger. Blackbeard not only renounced his Warlord of the Sea, title but busted the worst criminals in the world's history out of prison leaving the Chief Warden Magellan severely injured and Impel Down severely damaged. Whitebeard died, removing one of the Four Emperors, and all protections created due to his status, which not even the Marines themselves can handle; and Blackbeard went and stole Whitebeard's Devil Fruit, meaning the threat of the Tremor-Tremor Fruit (Gura Gura no Mi) continues with the power not in the hands of aging, morally-conscious legendary pirate, but an amoral, power-mad megalomaniac who just threw away his status as a privateer for the World Government in favor of being captain of the world's greatest sociopaths. On the other hand, both Coby and Shanks stop the war; Whitebeard's last words confirmed the existence of One Piece, keeping the age of piracy very much alive. With the Marines' victory, and Coby's words, this may encourage the organization to go through some serious changes, perhaps even ethically, to prepare for the new era. It's kind of a win-win situation for the Marines, and piracy in general. So the era of dreams isn't dead yet.
Yuusha-Oh GaoGaiGar FINAL, the Post-Script OVA to GaoGaiGar. It turns out the heroes only have the ability to open two tiny windows back to our planet that will stay open for a couple of seconds. They choose the two children to go back, entrusting the future to them. As they fly towards the portals, they pass by the ruined husks of all the Brave robots who sacrificed themselves using their ultimate attacks to save our universe, and hear each one's voice encouraging them to look forward and remember the Oath Sworn Through Courage. Finally, as they return to Earth and meet all their friends and family once again, the character version of the already fairly emotional ending theme begins to play.
Made even worse by the fact that, up to this point, the series was extremely lighthearted and took great pains to have everything come out in a happy ending. Throughout the series and FINAL, a total of two major human characters and one of the robot characters were killed. In the final episode, it is implied that every one of the Mobile Unit is dead for good, but it doesn't really matter because they and the rest of GGG are stranded in another universe. The viewer would not have been expecting anything like this, which makes it all like a kick in the stomach when it does happen.
An eventual happier ending is teased in the manual though. Specifically, Genesic GaoGaiGar's specs include a device called the "Galeoria Road" - where have we heard that name? Oh wait, it shares a name with the portal to the alternate universe in question, the Galeoria Comet. There's also what appears to be an old version of Guy himself who makes brief appearances in bonus content and Betterman.
Speaking of Betterman, it ends with Kankel being competely defeated by Betterman OLTUS' Psycho Birth, but as for the team: Shou and Kaede killed when Kaede suffered from Algernon, with her baby being carried off by Chandi, Miyako killed after she learned she was the carrier of Algernon from the first Dive inspection. Sakura lost her powers and is currently in a coma, with Keita and Hinoki ending up on a deserted island, just as they were in the beginning of the series.
Honey and Clover. Everything is going to be just right, except that the time at the art college leaves nothing but bittersweet memories for the protagonist.
Figure 17 ends with what might tentatively be called a Death by Newbery Medal: Hikaru vanishes at the end after defeating the Maguar for good because her human form was only ever temporary, and to top it off, Tsubasa has to leave all of her friends to move (again). But we do see that she's a much stronger person because of everything that happened.
Worst of all, "the adults" promised Tsubasa they would take Hikaru home and make certain that absolutely every scientific resource available to their civilisation would be dedicated to saving Hikaru from her eventual fade-out—they were practically about to take her back for the preservation attempt when the final battle blindsided them and forced Hikaru to burn off the little energy she was using to stay alive. Though, admittedly, there were subtle implications that Hikaru's life in the labs would not have been all too nice had she been preserved...
Akari from Aria finally graduates as a "Prima" and inherits Aria Company, but has to say goodbye to her beloved sempai Alicia, who retires from her job. She also sees her old friends a lot less than she used to.
Yokohama Kaidashi Kikou ends with the two main robots living together, tending to the coffee shop. But the main human couple have moved away to form a family, and it can be deduced that every human Alpha knows has already died by the time of the epilogue chapter.
The manga version of Chrono Crusade. The Big Bad is vanquished, but no-one truly escapes unscathed.
Not to mention the MASSIVE civilian casualties.
The anime version, too. It tends to be a matter of opinion what the proportion of "bitterness" to "sweetness" is. Joshua is so mentally damaged by what happened that he's mentally reverted back to the child he was before Aion corrupted him, and doesn't even remember Rosette and Chrono consciously, though he is otherwise perfectly happy and content and no longer suffers the ill-effects of being the Apostle of Hope, due to that power having been taken from him. All of the people from the orphanage have been restored to life. Rosette and Chrono retreat to a private cabin to spend the last of their days together in happiness, dying (at the exact same moment) hand in hand and smiling peacefully while sitting on a swinging couch on the porch. The epilogue to the anime, however, goes pretty heavily into Downer Ending; Father Remington, revealed to essentially be an angel in the series, may no longer return to heaven (though it's ambiguous whether he was exiled or whether he's chosen to remain on the Earth as a symbol of his disapproval for the suffering Rosette and Chrono were forced to undergo). In Rome, he bumps into a stranger and looks up to apologise- and, if only for a moment, sees the face of Aion. Seconds later, the man attempts to assassinate the Pope.
The first magical girl anime, Sally the Witch, had Sally exposing her powers to save her school. She was intended to eventually leave the Human World anyway, and thus had to say farewell to her friends, to return to the Magic World.
The ending of Kure-nai has Shinkurou successfully freeing Murasaki from the Inner Sanctuary, but he still must part ways with her when she chooses to stay behind with the Kuhouin family in order to fight against their traditions instead of continuing to run away. Murasaki's last lines were her realization that she never asked Shinkurou if he loved her.
Ichika from Uta Kata manages to save herself and the human race from being erased, but she has to say goodbye to the girl who has quickly become the most important person in her life.
In Bagi, the Monster of Mighty Nature, the eponymous human/lion hybrid gradually loses her humanity and goes feral. Then Ryo, the other main protagonist mistakenly believes she killed his mother, spends years training to get his revenge, and succeeds in stabbing Bagi. A minute later he finds he was mistaken, and that she had not only has not killed his mother, but actually carried out her last wish. The next day Bagi's body disappears, as she managed to recover, and ran away to the mountains, away from humanity
The manga Bitter Virgin ends with the primary couple Daisuke & Hinako together. But the hurdles presented by Hinako's traumatic past and its consequences leave little hope in everyone (including the couple themselves) that the relationship will ultimately survive. Daisuke himself thinks the job of taking care of Hinako should go to someone more mature than he is, while Hinako herself is certain Daisuke will find a more cheerful girl better suited to him than she is. But, in the here and now, they're together and happy.
I think part of the point of that ending is they actually will last together, perhaps better than other more sure couples. Its not they themselves looking for something better, its each believing they are not fit for the other. But to the eyes of the other, that someone better will never come along. They will spend their lives appreciating what they have as few others would. It may lead to some acts of self-sabotage, but what animanga couple doesn't do that?
Something similar to the example above happens in Koi Kaze. Nanoka and Koushirou are together, despite being brother and sister and the their ten years age gap, but the imagery surrounding them strongly hints that their relationship won't last.
Witchblade anime has Heroic Sacrifice variant. And that's right after Masane has Relationship Upgrade, her interaction with Witchblade sort of enhanced (though not without side effects) and she finally knows that Witchblade-induced transformation does not disturb Rihoko in the least. All the nice "Sisters" we saw are dead, others are ticking. Still, rogue X-Cons are wiped out, I-weapons are annihilated and Takayama is exonerated from blame, became hero and his rival isn't a threat anymore, so Rihoko is left in better world and good care.
Code Geass: Most of the cast gets moderate to happy endings, but the three protagonists that were instrumental in bringing about the peaceful resolution? Lelouch, despised by the world, is assassinated on international television, just as he planned; Suzaku, who impaled his best friend, becomes Zero, carrying the weight of the world's happiness even at the cost of his own, and must carefully hide his true identity for the rest of his life; and C.C. is still immortal, still wandering the world, and still lonely, although the knowledge that Lelouch genuinely cared for her (and never once blamed her for giving him his eponymous Evil Eye) was enough to give her the strength to live on.
Don't forget Nunnally, who watched her beloved brother die literally seconds after realizing he was a good guy all along. On the other hand, she regains her eyesight and becomes Empress, and she seems close to Suzaku in the epilogue, so it's not all bad.
And the same goes for Kallen who finally understood the truth about Lelouch just in time to watch helplessly while he is killed (Kallen's protective streak towards Lelouch is one of her character-defining traits). She gets everything she had been fighting for and is living happily with her bedridden-but-getting-better mother in a liberated Japan while attending school like a normal person, but she gets all those things at the cost of the man she would gladly have died for, and she's the one who narrates the epilogue in a rather bittersweet tone.
In Nightmare of Nunnally, Nunnally manages to save the world and regain her sight and mobility by rejecting her parents' plan, but that results in them vanishing from the world. Euphemia becomes empress, but her mission to restore peace to the world is hampered by hatred and distrust of Britannia. Lelouch is forced to leave Nunnally forever, but Nunnally has some comfort in sharing one last hug with him and him telling her he will always love her. Despite the problems that lie ahead, Nunnally still believes that there is hope, and is willing to face the future with her best friend, Alice.
Sola: Aono is turned back into a human, but this requires Matsuri to sacrifice her own life. Plus, Yorito dies as well, and Aono removed herself and Yorito from the memories of Mana and Koyori.
Death Note: The series' Karma HoudiniVillain Protagonist finally gets his just rewards, but way too many people died in the process, and millions of people around the world still revere him as a god.
On the flip side: humanity lost the first real chance for world peace ever and all those people died for naught.
Fullmetal Alchemist ends with Ed and Al both alive, but stuck in parallel worlds.
The movie's ending is arguably bittersweet as well. Ed and Al finally get together again, but they're both in the parallel world for good. The brothers thought little of leaving their friends behind forever, which was especially heartbreaking for Winry. While Ed didn't really have a choice and decided to make sure the Gate could never be opened again by doing so, Al did.
Osamu Tezuka's Metropolis ends with the main character Kenichi stopping world domination...At the cost of his love interest Tima, a cute synthetic human girl who was used as a superweapon, driven mad by the effects of it and winds up falling to her doom despite Kenichi's futile attempt to save her. Oh, and he decides to stay in Metropolis while his uncle returns to Japan. The we see a radio in a junkyard, and we hear Tima's voice saying "Who am I?".
In The original Japanese release and the English Theatrical release of the film had a picture after the credits depicting a shop named "Kenichi & Tima Robot Company," with Tima visible in the window (or possibly driving the truck as the person looks similar to Tima). This could imply that Kenichi succeeded in rebuilding Tima (even though it would be unclear whether he had managed to reactivate her), or the Tima in the window could only be a painting or picture. Not to mention, it wouldn't seem like a good idea to reactivate her.
5 Centimeters Per Second: Takaki finally takes control of his life and starts to deal with the lonely and bitter feelings that he's been nursing for fifteen years, and he has a chance of finding Akari again. But he has no job, no girlfriend, and the Akari prospect is uncertain and would require breaking up another relationship.
Now and Then Here and There has an ending that is positive, but heartbreaking. "Can we watch another sunset together someday." as the girl speaking fades out of reality as the price for having saved the protagonist.
Subverted in Kannazuki no Miko. In the last scene it appears that Chikane is going to stay locked in the shrine, never to see Himeko again; but an additional scene after the ending credits shows the two girls meeting on the street again.
It isn't quite clear though when that happens, so they both might still have waited for a long time—especially considering Chikane has to be reincarnated and grow up once more.
In Yu-Gi-Oh!!, the finale ends with the pharaoh gets to learn his real name and going to the afterlife, but he must leave the friends he made here.
Digimon Tamers ends with the Tamer's partners de-digivolving and then being forced into the Digital World, and the Tamers are left to believe that they will never see their partners again. It would be a downer ending, except for the last five seconds or so before the ending credits, offering a bit of hope that they will be re-united eventually.
That hope is subsequently dashed to pieces by a later Drama CD which has the Tamers blindly sending messages to the Digital World in hopes of maybe reaching their partners.
This is par for course for Digimon, really. The normal ending is "heroes kick the butt of the Big Bad, Digimon have to return to the Digital World and leave them behind". How much hope of a reunion varies heavily. Digimon Adventure 02 is the only series thus far to not end this way.
Parts 1, 3, and 5 are pretty bittersweet. In Part 1, Jonathan defeats Dio, but at the cost of his own life and the lives of everybody on the ship except Erina and an infant. To make it worse, he doesn't even succeed; Dio takes Jonathan's body in order to survive. In Part 3, they do finally kill Dio, but half the group dies in the process. Part 5 ends on a similar note to Part 3.
Part 6 ends on a very bittersweet note. Emporio defeats Father Pucci, the Big Bad, but he's the only hero who survived Pucci's Stairway to Heaven stand. While there seem to be copies of the others in the new universe, they have no memories of their adventure or of each other. Only Emporio remembers what happened.
Hell Girl's second season, Futakomori, ends with Ai dead, but the souls of her family finally at rest.
Strawberry Panic spends its final few episodes building up a sad but beautiful Bittersweet Ending — only to swerve away at the last second.
Hitohira has the Bittersweet Ending that is so typical for high school series, when a large part of the cast graduates. This is put up a notch by Mugi being left behind by her best friend who studies abroad and that her sempais made lot of difference in her life by giving her more confidence. The beautifully envisioned farewell scene between Mugi and Nono on the rooftop is absolutely heart-wrenching--and the last shot of the names of all five members of the Drama Research Society carved in the old club room door seal the bittersweet mood once and for all.
Karin has one of these as well. Is finally allowed to marry Kenta and live as a human, but her family erases her memory of themselves so that this can happen
In the anime of AIR, Misuzu dies at the end from her curse, but managed to reconcile her relationship with Haruko before that in a particularly heart warming series of scenes. Furthermore, since she found true happiness by meeting Yukito and coming to love Haruko, Misuzu apparently broke the curse on Kanna, ensuring her next reincarnation cycle will be a normal, happy life. Meanwhile, Yukito is stuck to live the rest of his life as a Crow... In the anime/manga anyway. In the movie he leaves town in the end, promising to help Misuzu the next time she reincarnates. The Manga ends quite a bit happier, with Misuzu surviving.
This Ugly Yet Beautiful World manages to avoid the expected Gainax Ending, the world is saved... but Hikari and Akari have disappeared, heading across the vast reaches of space in order to help find a home for all the life energy released during the averted Apocalypse. The song "Kimi ni Aete" which plays over the ending, coupled with the new star visible in the sky as proof of their existence makes this quite the Tear Jerker as well.
The manga version of Elfen Lied. Lucy dies, and Kouta ends up marrying his cousin. Millions of children, evil Dicloni, die as well.
The "Tower of Paradise" arc in Fairy Tail ends on a bittersweet note that's more "bitter" than "sweet". Sure, the Tower was destroyed and Erza's former Nakama were freed (and reconciled with Erza). However, Simon died in a Heroic Sacrifice. The Reveal at the end of the arc makes it dangerously close to a full Downer Ending: the real villain of the arc, Ultear, got what she wanted out of the whole mess (discrediting the current magic council, so they had to disband), while Jellal (the apparent Big Bad who they actually beat) turned out to be nothing more than her brainwashed pawn! Oh, and it turns out the Tower never could have revived Zeref, or rather did not need to, because Zeref isn't actually dead. Jellal's rampage gave Ultear's real allies, the Dark Guild Grimoire Heart, the chance to acquire one of the keys to Zeref's seal.
Nanaka 6/17's got one—while the teenage Nanaka does begin to grow as a person and her relationship with Nenji gets back on track, the child Nanaka is essentially dead and Nenji's not sure which one he prefers. Fortunately, there's the Bonus Episode which doubles as one big Crowning Moment of Funny to offset it.
Full Moon o Sagashite's ending is quite a Tear Jerker. After it was revealed a bit earlier that Eichi 's soul was with Mitsuki all the time, enabling her to see the shinigamis in the first place, we see Mitsuki after her operation. Through a miracle, or rather a (not that heroic but still) Heroic Sacrifice of Mystia and Jonathan she still hasn't lost her voice yet and is singing at a concert, when suddenly Takuto, who was thought to be dead shows up and they're happily reunited... ...until the camera pans to Eichi, who separates his soul from Mitsuki's body and is seen flying away reaching out for her while crying. Until he eventually calms down, smiles down on her peacefully and vanishes into nothingness.
This is probably made even sadder by the realisations that with Eichi gone, Mitsuki is now unable to see or talk to any of the shinigamis ever again; not to mention that she's only still alive because of his presence and the ensuing events, which means that he himself ruined his chance to be reunited with her in death any time soon.
The ending of Eureka Seven: Pocketful of Rainbows can be considered bittersweet. Though the heroes manage to save the world, the members of Gekko State are all doomed to die early due to their accelerated aging, the government's Kill Sat causes untold collateral damage that kills countless innocent people, and Eureka herself was forced to sacrifice her memories to save Renton and become an ordinary human being who is incapable of speaking, thanks to memory wipe.
The manga ending is even worse. Although Big Bad was eventually defeated, Eureka dies in Renton's arms from her wounds. This leaves him and his grandpa to look after the 3 kids for at least 2 years. Thats gotta suck for a 14 year old kid.
In Hanbun no Tsuki ga Noboru Sora, Rika survives the difficult heart operation, but only has a few more years to live regardless.
The ending of Solanin. By this time, it seems that the group has finally somewhat come to terms with Tsuneda's death and Meiko has decided to get another job. However, Ai might be leaving for Sendai which threatens her relationship with Kato who in turn isn't doing well at his job and none of the band members have the motivation to go beyond occasional practices. On top of that, the general sentiment seems to be that life sucks and is boring so you should cherish what small happiness you can get out of it.
Tsubasa Reservoir Chronicle. The Big Bad is finally killed, but that in turn means that his creations, Clone!Syaoran and Clone!Sakura can no longer exist. All existence as we know it is falling apart, and the only way to stop it is for Watanuki to be stuck in one world (the shop) and Syaoran Jr. to constantly move between worlds, meaning that both of them will put strain on the relationships of their loved ones. Thankfully, Syaoran Jr. to makes the most of his price by deciding to look for a world that can bring back the clones. Unfortuately, though Watanuki looks like he's coping well enough, it doesn't look like there's much hope for him on the XxxHolic side...
Video Girl Ai sets up for this trope only to subvert it when Ai is rematerialized as a human right after what seemed like a tearful final goodbye in the epilogue. Crowning Moment of Heartwarming ensues.
In a way the Anime Fanbase received a rather harsh example of this trope. For years many of us wanted to put an end to Macekres and Bowdlerization in Anime English dubs (in which companies such as 4KidsEntertainment are known offenders). Hackjobs are becoming far more rare in Anime English dubs as the uncut accurate ones are truly becoming the majority. Alas this was starting to happen more since the mid 2000's when Network Decay became a known epidemic. So while there are substantially less hackjob anime dubs on TV the amount of anime dubs on TV in general is not that much better. Doesn't help that a few of the known Anime Dub companies are dead and most of them are struggling to not follow suit. So to make a long story short, hackjobs are occuring few and far between but the anime industry isn't exactly doing better.
The opening scene of Fang Of The Sun Dougram strongly hints at a Downer Ending, but it turns into a bittersweet one at the last moment. The civil war seems lost when the Big Bad tricks of the La Résistance leaders into accepting his very unfair offer of independence. Most guerillas go home and the Liberation Army becomes a police force and the handful of rebels who see through the deception and continue fighting are surrounded by the Earth Federation Military. Then suddenly the Big Bad gets assassinated and the tricked rebel leader takes a stand and refuses to let the earthlings run his newly-formed country. In the end, the planet Deloya is still only formally independent, the eponymous Humongous Mecha is destroyed, but it's heavily implied that future prospects are bright.
During the final battle in Akumetsu, Shiina is shot and is bleeding to death. In order to save her, Hazama Shou sacrifices his own body to create a clone body for Shiina. He uses his Akumetsu mask to transfer Shiina's mind from her dying body to her new body. Shiina is able to survive, however, all of the Akumetsu/Shou clones die at the end, and the clone plant is also destroyed.
Starship Operators. Amaterasu is destroyed, and Kibi does not regain its independence. The cast do get the Earth Federation to declare war on the Henrietta Alliance of Planetary Nations... but they're only interested in taking the planets of the Henrietta Alliance for themselves. Even then, they managed to unite other remaining independent planets against the Earth Federation after their last newscast.
Tekkaman Blade. The Radam invasion has been prevented, for now. Unfortunately, in the process D-Boy had to kill the rest of his family and friends that weren't already dead as a result of the initial Radam attack, except for his sister who was killed off by his younger brother. Fortunately, fighting as Tekkaman Blade has damaged his brain to such an extent that he no longer remembers that he ever had a family, or what he had to do to them.
Episode 14 of Tokyo Mew Mew, which focuses on Keiichiro and his ex-girlfriend, shows them coming to terms with their breakup and parting ways forever rather than getting back together.
Muhyo and Roji manage to defeat Ark and convince Enchu to make a Heel Face Turn, but Enchu accepts responsibility for his actions, and is sentenced to life without parole.
Monster ends with Johan being incapacitated, Tenma being exonorated, and Nina returning to as normal a life as she possibly can. Mostly everyone else is dead.
Everyone being Wolfgang Grimmer. Still, it's also worth noting that the incapacitated Johan may not be so incapacitated at all, even though all the living earn their happy ending.
Fafner in the Azure ends with a number of the pilots dead, Tsubaki must tearfully say farewell to her friends before assimilating with the Island, and Soushi dies even after Kazuki saves him. At the same time, Tatsumiya Island has the information to save Sakura's life and prevent the early deaths of the pilots, the world's civilizations can rebuild, and Soushi promised Kazuki he'd find a way to return one day. Judging by the trailers for the movie, he will.
In addition, there's the even more bleak prequel special. Yes, Tatsumiya Island obtains data from the wreckage of Ryo's Titan-type Fafner to fight against the Festum and the Island now has time to prepare for the upcoming battles, but most of the important people who do survive are going to die soon enough anyways and everyone who partook in the L Plan were killed as well.
Cowboy Bebop, a show where most of the episodes are standalone, has almost every other episode end on a bittersweet note (Asteroid Blues, Waltz for Venus, Jupiter Jazz, Speak Like a Child, Boogie Woogie Feng Shui and Black Dog Serenade, to mention a few). The main character arcs of Spike, Jet, Faye and Ed that get absolved in the last three episodes could be considered to end either like this, or as downright Downer Endings: Two of them discover that You Can't Go Home Again, and the other two lose people close to them.
Samurai7. The samurai save the villagers from annihilation by the bandits and Ukyo, but at the end of it, four of them are dead, and none of the other three stick around.
Neon Genesis Evangelion. After everything the protagonists do to kill the Angels and prevent the extinction of the Human Race, it happens, leaving only the main hero and a love interest around in a gestalt. Possibly subverted by the fact that everyone else can come back if they want, we just never see any of that happen.
Also occurred in Sonic X. The cute little kid who spent most of the series in a state of perpetual Survivor Guilt was dead after sacrificing herself to save the galaxy (Because Destiny Says So), while making her potential love interest the one who had to shoot her in a scene which would bring tears to the eyes of hardened criminals, the human cast member had to go home, had no time to say goodbye and would probably never see any of them again. Plus, Shadow is off somewhere brooding in space—again—but hey, at least the universe was saved.
Arguably the ending of Gregory Horror Show: The Second Guest, though more on the "bitter" than "sweet." The female protagonist finally has what she's been wishing for--a family to call her own. Meaning a husband a child to look after. On the bitter side of things though, in getting this, she's become a permanent guest of the Hell Hotel, cannot go back to the real world, and lost her sanity/sense of self in the process. Oh, and it'sGregoryshe's got a family with.
In Satou Kashi no Dangan wa Uchinukenai, the aloof middle-school-aged protagonist Nagisa decides to go to high school after all and her brother overcomes his illness but only after Nagisa's friend Mokuzu's gruesome death.
Macross Frontier does this in the Non-Serial Movie: The Hero Dies, as dies one supporting charachter, one Idol Singer is in coma and possibly up for A Fate Worse Than Death, the other is heartbroken. But all other good charachters survive as does Frontier, they find their planet, all baddies are killed, and the comatose charachter at least has some signs of recovery - and this after it seemed they would get a Kill'Em All ending. Life goes on and the galaxy as whole is safe for now. Two (+1?) lost lives for the whole galaxy is a good trade, or is it?
Actually ultimately subverted. Word of God confirmed that not only is Alto still alive, but that Sheryl makes a full recovery. He was actually shocked by how pessimistic towards the ending most fans were.
The ending of Ressentiment - the main characters manage to avert a nuclear holocaust and give Moon a new life in the real world, but on the other hand, none of the characters' issues get resolved - fifteen years later Takuro is still a lonely loser, Nagao is a single mother with an even longer string of failed relationships behind her and Echigo is dead.
The ending of Puella Magi Madoka Magica. Madoka becomes a Puella Magi, changes the whole system so that witches no longer exist and brings Mami and Kyouko back to life... but disappears from existence as a result. And even though witches no longer exist, a new threat has replaced them because the Incubators still need to collect energy from some place to keep the universe's gears turning. The meguca battle never ends...
BUT... it's also assumed that Madoka became a Goddess from the result with Sayaka and the girls that were originally witches had Ascend to a Higher Plane of Existence, essentially making it the magical girls answer to Valhalla.
Blood Plus could be argued as having a Bittersweet Ending. Diva dies, Saya lives after trying to kill herself on Diva's blood but is deeply affected by her death, Hagi is crushed under a building, Riku's rape and subsequent death at Diva's hands still haunts Kai and Saya, and Solomon died for Saya without her even knowing. A lot of people are dead, including huge numbers of the Red Shiled, and all but one of the Schiff, and the kind of emotional and psychological toll it has taken on the main characters is palpable. However, there are still some good things. Diva's children are being looked after by a loving and caring family so they won't turn into monster sociopaths, Kai is getting on with his life, Lulu is still alive, and Julia is pregnant. At the end we see that as Saya goes into hibernation again, that Hagi's trademark blue hair ribbon is by her sleeping place, indicating that he is still alive and waiting for Saya to awaken again. So in the end, this becomes more of an Earn Your Happy Ending type of story. Considering the kind of pain and grief the main characters had to go through to get it, they really do deserve it.
Several chapters of Helen ESP end this way, such as "Helen and Devil", where the dog Devil is beaten to death, but the baby it was caring for survives.
At the end of Canaan the eponymous character, and her very close friend (or more, as its implied), Maria go their separate ways because they're lifestyles are too different for them to stay together.
The ending of Mirai Nikki certainly counts. Sure Yuki and Yuno were able to become god of the 3rd world and the memories from Yuno of the 2nd world were given to 3rd world Yuno. However that doesn't change the fact that everyone with the exception of the 9th, the Muru murus, and Yuki himself (obviously) from the two previous worlds are dead. Also, neither of them can just hit the reset button (as Yuki painfully became aware of) to bring them back totally. All that would come back would be their bodies, not their minds. Seriously, were it not for the 3rd world resolving the way it did, the end would have been a full blown Downer Ending.
Jyu-Oh-Sei: Thor has finally acquiesced to Tiz's insistence that he be her husband, and he successfully stops the Big Bad's plot... but his best friend, Third, kills himself, and Tiz ends up dying in an even more thoroughly pointless fashion.
Angel Beats. In the anime at least, it ends with EVERYBODY in their world disappearing except for Otonashi and his closest friends. Then, once it's down to two (Otonashi and Kanade) there comes a revelation that a lot of people saw coming a mile away, but still, Otonashi's crying and despaired scream as the last word of the show (aside from ending themes) was pretty depressing. Not to mention that the song that plays for the last few minutes of the show, Ichiban no Takaramono, is pretty sad in and of itself.
Popotan ends with the sisters still on the same journey through time that has caused them so much grief throughout the series, but now they've at least grown to appreciate being together. The ending is more happy than sad to be sure, but not enough to not qualify for this trope.
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