When Mitsuru first calls Yukari by her given name, especially given the namingformality of Japanese society.
This Troper will admit to nearly crying at the end of Persona 3. You're made to think that your entire team has forgotten about their adventures together after defeating Nyx when suddenly, during Mitsuru's speech on Graduation Day, the promise that you all made together brings it back. Mitsuru stumbles in a speech for the first time in her life, Akihiko pulls Yukari and Junpei out of their seats towards the stage, and (after recovering from her slip-up) Mitsuru - who'd previously been the emotionless, precise bookworm - jumped off the stage IN FREAKING SLO-MO and greeted them all, practically crying. Best. Ending. Ever.
Expecially if you did the bad ending which is all about thinking about today and not worry about the future; heartwarming as the character in this ending realise that you don't live life to its potential this way, so they proceed to reclaim this potential
And even more heartwarming, is Aigis' tear as the hero finally leaves his body behind (dies) as the rest of the group is running up the stairs to the roof. "The Path is Open" will forever bring tears.
If you visit the fortuneteller at Club Escapade during the Playable Epilogue, she will tell you that you have infinite possibilities, and that there is nothing you cannot do, nothing out of your reach. It's a wonderful feel-good message, after all that has happened... then you realize what is about to happen to you, and... yes, "The Path Is Open" just becomes beautifully liberating, and poignant.
On September 23rd, ask Shinjiro to the movies. it's a heroic animal marathon. And if you've been paying attention so far, you'll know he loves animals. At the end, he starts to cry, and runs away. It was one of the best moments of video gaming for this troper..
The ending to The Answer also qualifies. After everything that's happened, the whole cast really has become very close. Aigis has become more or less human, she and Yukari have no animosity, despite what happened earlier, and then the credits and New Day start playing.
For anyone who played through Persona 3 already, playing the Portable remake as the female protagonist is nostalgic, but lightening in the fact she becomes much closer to SEES member through her different social links with said members improving the whole Nakama aspect. One that stands out though is the Moon Arcana Shinjiro Aragaki's Social Link. Through their interactions together, the heroine learns that Shinjiro is actually not that much of a jerk and more of a Type B tsundere, only to easily and often be irritated by Akihiko. He does care for everybody in SEES, but knows that being close to them would result in pain for them that he'd be more than happy to prevent by acting like a jerk. In later ranks, he hints that his days are numbered, but wants the heroine to accept what happens. in the final rank, he tells her that now he has nothing to worry about (SEES) and that he believes in her to lead SEES. It's surprising how much 10 moments with a Guest Star Party Member can be so touching.
Eleven moments if you choose to become lovers. There's something really heartwarming (and even a little funny) seeing the resident Badass get flustered when the girl he likes confesses her love and asks to go to his room.
On new game plus, if you managed to get Shinjiro as a lover, talking to a girl in your classroom will prompt her to say that Shinjiro woke up from his coma and escaped the hospital (to find YOU, the female main). On the very last day of the game, you can choose him to be at the heroine's side as she fades away to become the seal instead of Aigis. He musters enough strength to embrace the female main, and his final dialogue is very touching.
Shinjiro: "...I'm glad to have met you."
All of Shinjiro's links are like this, especially the ones closer to ten. In the 9th one, he basically tells you he'll be dying soon, and he asks you not to cry, as well as to forgive everything else -- including Ken, who he knows will want revenge. The FeMC didn't cry, but I did.
If you max out Shinjiro's Social Link before October 4, it was stated by Shinji's extra dialogue that the FeMC DID cry when she saw Shinji blood-soaked on the floor. (Apparently, he was telling her not to.)
Also from the female's path in Portable, the end of Ryoji's Social Link.
"If I could stay like this I'd probably...stay with you forever."
Speaking of the female protagonist's route, having her become Akihiko's girlfriend in time for Christmas provides a lovely little scene in which the two of them spend Christmas Eve together. Akihiko presents her with the gift of a music box, and promises he'll give her something new to put in it every year... a deeply touching statement considering that they've spent all December contemplating the coming of the Big Badand the unpreventable end of the world, and that at this point they have no guarantees that any of them will live to see spring.
Getting Akihiko to be the female protagonist's lover, if you triggered the right event flags. It's the joy you hear in his voice when you say yes.
Let's not forget about Ken. After the October incident, what he's living for (outside of finishing what he started) is for your approval/love. His romantic route, while it may be squicky for some, has some genuinely sweet moments. In fact, he says "I love you," multiple times (Rank 10, Christmas Date and March scene), promises to take her on trips when he's old enough (and that's on the Christmas date which is heartwarming for similar reasons as Akihiko's above) and on a more sad note is the only one that seems to notice that the protagonist performed a Heroic Sacrifice and asks not to leave.
The Answer is filled with these. Mitsuru comforting Yukari, Metis realizing that Aigis accepts her, Yukari reconciling with Aigis, Mitsuru choosing not to take everyones' Evokers, Yukari wanting Aigis to be her roommate...
I don't know about you guys but this troper found Mitsuru's social link quite adorable.
Especially if you're playing as the female.
Oh god yes.
(while getting ready to watch a horror movie)
Mitsuru: W-would you mind..if I held your hand?
It's also a funny moment, as the female main character is practically shoving the DVD in Mitsuru's face. Mitsuru is...actually rather nervous.
Koromaru's social link. All of it.
>This must be Koromaru's resolution. Koromaru will follow you for sure...no matter where that might lead. That's how you feel.
There's a minor one that hit this troper when he was checking out his social links during the last month to see Shinjiro's name listed in the Nyx Annihilation Team, despite the fact that this was created after his passing. Gone, but not forgotten, indeed. His name is also never removed from the Fool Link either, causing this one to count double.
Two days before the final battle, Koromaru will ask you to go out with everyone. You are then treated to a scene with everyone playing together at the shrine playground. Yukari and Mitsuru disscussing clothes shopping, Junpei and Fuuka horsing around, Ken and Akihiko playing on the slide and Aigis teaching Koromaru a handshake. It's potentally a last moment together with the team and they're all enjoying it. *sniff*
Another small but somehow heartwarming thing: All through the month of January, while Takaya's cult is gaining followers left and right and it seems like everyone you talk to is either buying into it or giving in to despair, every teacher at Gekkoukan speaks up against the cult and its doomsaying during their class lectures.
At the end of the game you get to meet Akinari's mother on the same bench Akinari sat on what would have been his 20th birthday. It's both a tearjerker, yet heartwarming. "Only 19 years...it wasn't long enough. He was almost an adult, but he never made it. Every day, I wondered if he'd wake up the next morning...I blamed myself for what he inherited..." Yet at the end of his life, Akinari, smiling, tells his mother he was glad to have been given life and her son. And his mother found joy in his life too. Even though she's lonely, her son inspired her to keep on going, looking straight ahead. The most heartwarming part is her promise to do everything her son couldn't do, and tell him everything when they meet again on the other side. And you tell her he finished his story, her only regret being he never finished it. She decides to wait for him to tell it to her himself, having something else to look forward to. She leaves with some advice that everyone can relate to: "Take good care of the ones dearest to you. If you wait until their time has come, and you're clinging to their cold bodies....then it's too late." Those who thought Akinari's Link didn't suit The Sun, this scene proves them wrong.
Also, the same troper finds just Akinari's smile heartwarming. For a dying young man, that smile conveys so much life and happiness...
The female route, Junpei's social link at rank 9. He finally finds your stalker and got into a fight to get the perpetrator to stop taking pictures of you. After explaining this, Junpei goes on to also say that he feels like he's become a better person after knowing you, and realizes that people aren't perfect, everyone has a little bad and a little good in them. He then explains his actual reason behind tracking down whoever was passing around pictures of you: "I guess in the end, I wanted you to trust me. Like, if someone like you could trust me, then I might be worth something..." (This also bordered on tear jerker for me, since I'd gotten this scene closer to the end of December, where it seemed like everything was going wrong. After seeing his life turn to crap, and him getting mad at me over small things, this scene made me think we were still bros for life, in spite of the obstacles.)
For those who played Shin Megami Tensei III Nocturne every time you cast Best Friends feels like this Forneus is first boss you MUST defeat to get out of starting area. In second area there will always be Decarabia waiting for him and there is no way for you to tell her that he is dead. And seeing them finally reunited, in a different game and different time gives this troper a nice and fuzzy feeling that they are finally together