Assassin's Creed II has several powerful moments, especially at the beginning, where Ezio watches his father and two brothers be hanged. Later on, reading some of the letters to Templars from their family members can be heartrending, especially Carlotta Moro's letter to her mentally-handicapped former husband, Dante Moro.
Another incredibly sad bit from ACII is the final The Truth video, where you hear what were probably Subject 16's last words before he committed suicide: My mind is gone. Lucy, I can't wait any longer. I'm ready to go now. She sees me raise the knife... Especially sad due to the contrast to the earlier Truth videos where Sixteen is barely managing to hold himself together due to the trauma of extended stays in the Animus. This time he is completely calm, and at peace.
The first Asssassin's Creed game has a Tear Jerker, but it's for one of Altair's victims, all of whom are undoubtedly evil men. Having said that, Sibrand's death is rather sad. In an eavesdropping event and just before you kill him, you see Sibrand as an incredibly paranoid, vicious man who kills an innocent priest under the belief that he's an assassin sent to kill Sibrand. He's ranting and raving as he fires arrows into the air as you approach, but when Altair finally gets him, he quietly begs the assassin not to kill him. It turns out due to the Templars discovering the Piece of Eden in Jerusalem has proven to Sibrand that there is NOTHING after death. No heaven, no hell, nothing, and he's terrified of what's about to come. It puts all his crazy paranoia and ranting into perspective. The knowledge that there is nothing but darkness waiting for him has effectively destroyed Sibrand, long before Altair came along. Despite the fact that he, like all the other Templars, is a monster, every time I hear him say 'Nothing waits', it makes me feel bad for him.
The last codex in ACII is Altair's last writing, where he says he's not long for this world and doesn't think there's anything after this. After a whole game, a little scene in the middle of the 2nd game, and 29 codex pages you've come to know this man very well and are now reading the last thing he wrote before he died.
And then come Revelations, where you, the player, will lead Altaïr himself to his death in the 6th and final seal memory:
Sit a moment and rest...
Brotherhood has series of massively hard-hitting ones in Ezio's repressed memories of Christina.
The first is immediately after the execution of Ezio's brothers and father, where he has to carry their bodies to a boat to give them a proper burial. One can tell from the way Ezio is talking and moving that he's felling hate and rage and grief but is holding it tightly in check...and then he has to tell Christina he is leaving.
The next two memories go hand-in-hand, with Ezio returning to Florence and discovering Christina in an arranged marriage. She still loves him, and wants to go with him away from the marriage, but Ezio knows his quest for revenge makes it impossible for them to be together, and he gives her a long, passionate kiss as a farewell. Then, the next memory starts years later with Christina in Venice, and Ezio masquerades as her husband to steal a kiss from her. She takes off his mask, discovers Ezio, and the subsequent scene has a heartwrenching What the Hell, Hero? moment as she yells at Ezio for leaving her to her marriage despite the fact that she loved him. The heartbroken look on Ezio's face is the real kicker.
The final memory is the worst, as Ezio returns to Florence during the Bonfire of the Vanities to discover Christina being attacked by Savonarola's men, and she is mortally wounded. Ezio takes her into a small garden, and as she lays dying in his arms, he tries to apologize for never being with her. She tells him he was always with her, and gives him his necklace back. It ends with the single most gutwrenching use of Ezio's Catch Phrase ever.
Requiscat in pace... my love....
What got this troper was his line as he sprints at Crisina's killers: "CRISTINA! RUN!" Hearing the normally cocky and suave Ezio Auditore de Firenze scream like that sent chills.
There's one more immensely subtle element of the Christina memories: the "Christinas" that Ezio interacts with in Rome to trigger the memories look like Christina, but if you examine them closely, they're just young women who happen to resemble her in hairstyle and dress. And you know how, after you lose someone close to you, you keep seeing their faces in a crowd? Ezio seems to keep seeing Christina while walking around Rome. No wonder he is so intent on rescuing Caterina from the Borgia. He still hasn't gotten over Christina's death, poor guy.
In the final sequence of Brotherhood, Desmond finds the apple of Eden, and the world freezes as soon as he picks it up. The apple directs him towards Lucy, and with his hidden blade drawn then gives her a stab in the stomach. The two fall to the floor, with Lucy bleeding heavily. The screen then goes black, and the credits roll, making millions of players across the world shout "Damn it!"
It's especially distressing that the player has to mash a button while the scene plays out, ostensibly to resist what's happening, but no matter how fast you press the button you draw ever closer to Lucy. By making the player do this, it puts them in Desmond's situation in a very real way--trying with all of your might to resist something, but no matter how hard you try you can't stop it.
In Brotherhood, completing all the glyph puzzles reveals the origin of the voice in the Animus: Subject 16. Compiling subsystems. Infrastructure. Tendons. Heart.Voice. All that whispering about being lost and alone was Sixteen trying desperately to claw his way into consciousness. After all his suffering, he still can't die - can't let himself die - because he has to help Desmond. And with all his energy he can only make contact for a few moments at best. Like Desmond, Altair, and Ezio, he has a long, terrible path before him, but unlike them, his continues even past when he should finally be at peace.
Project Legacy gets pretty damn depressing in places.
The implied fate of Fiora Cavazza, as seen through the eyes of a child, ends on a very bleak note.
I ask Papá if he will hurt her. He tells me he will.
Similarly the whole sequence of Giovanni playing with his "aunt" Lucrezia highlights how much he's taking after his father, and goes straight for bittersweet at the end.
I ask Zia about my Mamma, if she knew her. She says she did. My Mamma was young. Too young to know what she was doing. I ask where my Mamma is now. Can I meet her? She says she does not know, but she does know my Mamma loves me.
In Brotherhood, this troper got a bit teary eyed when his recruits died. So far (as of sept.10, 2011) he has lost 7 brave warriors, 4 in combat and 3 oversea. I've been only been able to close the eyes of one. Number 7 is actually more of a Forgotten Fallen Friend as his name I can't remember.
In contrast, this troper only lost 3 of his recruits, but felt just as downhearted about them, especially the one who died thanks to his careless use of the Apple of Eden.
This troper lost just one recruit, her first and only mistake, because she rather foolishly plunged deep into enemy territory when she decided to take on one of the most difficult Borgia Towers before she was ready. What hurt most, more than the fact the Borgia Captain fled and the recruit effectively died in vain, was the fact I had no choice but to run and leave the body of my fallen recruit down in the tunnel... I never even got to close her eyes.
This troper was shocked when he checked the pigeon post only to find two empty slots where recruits should have been. None of them had been sent on difficult missions, the odds were always stacked in their favor, 80% odds of success minimum...and yet two of them didn't come back. It felt like I failed them...
The entirety of Embers. Or more specifically seeing how close Ezio is to death. Although he's certainly able to keep up with Shao Jun and take out a few Chinese mooks (Including a Juggernaut mook), it's clear that death is coming for him. And at the end of Embers, it does.
Revelations actually has quite a few Tearjerker moments in the final third of the game:
The third Altair memory with Maria's death and Altair's exile
Made all the worst if you read the novel The Secret Crusade, where the Altaïr memories are taken from. In the novel, you learn what happened to Malik, especially concerning what happened in Masyaf while Altaïr had been in the East dealing with the Mongols with Maria and Darim. Malik is accused of Sef's murder and is imprisoned, thus allowing Abbas to built a council of Assassins in which he leads to take over the Order. When Altaïr returns he confronts Malik in prison and learns the truth, frees him, and goes to confront Abbas. Right before he hands Abbas the Apple, Altaïr is thrown a burlap sack. It's Malik's head...
Ezio discovering Yusef's body in the Assassin's Den and quietly saying something akin to "You have earned the rest, Brother.
The final sequence where Ezio discovers Altair's final resting place and the final Masyaf key. Manly tears were shed. "Sit a moment and rest..." indeed...
Abbas's death. Just seeing him finally concede that Altair is the better Assassin, and finally accepting that Altair told the truth about his father's suicide, which is pretty much the only thing that made him take over the Brotherhood and drive Altair into exile. Especially when he wonders if he can see his father again and ask him if Altair was right.
For this troper, the fact that Ezio lives his whole life in search for answers after his family's execution, and in the last moments of Revelations, it's revealed to him that answers will never be his. His purpose is simply as a messenger, to pass the information on; he himself won't be granted the knowledge. It's this moment where he chooses to put the Assassin life behind him.
Revelations was, to this troper, emotionally heavy through and through. From this being Ezio's last game to the deaths of beloved characters, what really makes the Tear Jerker hit critical was the end. As in, the end of the world. Here we have the first civilization, and then that solar flare. To all of those people, their whole world came crashing down on them, and the camera seems to love to focus on a young mother and her baby, right up until a wave of fire engulfs them... Combined with the music, one can't help but feel goosebumps after watching it. And not just the first time either.
While it's not techinically canon, if you fail in the mission to rescue Bartolomeo's wife from the Baron De Valois, you get a nice little scene of a gun being lowered to Pantasilea's head and her brains being blown all over the wall. If nothing else, it's good incentive to be more careful next time.
Very early into Brotherhood, the attack on Monteriggioni. After killing a bunch of invaders on the outer wall, Ezio sees Cesare about to shoot Uncle Mario. He races across the rooftops, but he is too late. After we're assured that the enemy only has guns because they're holding Leonardo hostage, two gunshots go off, wounding Ezio and killing Mario. The three remaining Auditore are forced to leave the villa through an underground passageway, and you'll have to go the rest of the game without the armor of Altaïr.
The backstories of some of the multiplayer characters fall under this for this troper as well. Personal favorite would be Vali cel Tradat, aka The Sentinel, if only for his death speech:
Once your Creed was as vital to me as air and water… but when the Turks marched into Wallachia, and you Assassins did nothing to stop it, how could I continue to believe? If a man's philosophy does not let him protect his people, his home, and his family… what good can it do for the world?