Despite the fact that he agrees that Teruteru wasn't justified in committing murder, when Teruteru's door is examined after Chapter 1, Hinata still makes a promise to his friend that he will find out what happened to the Hanamura Diner and come back one day to tell him.
Similarly, while Mahiru never got along with Teruteru, and also agrees that his actions weren't justified, she knows perfectly well how he feels about his mother, since she believes that "your mom is your most important family." The cast might bicker and be driven to murder one another, but that doesn't mean they don't have sympathy for each other.
Hiyoko, who is a pain in the ass to pretty much everyone sets up a memorial for Mahiru after the latter has been murdered.
Then in a bonus scene after her initial attempt flops, she arranges for Hajime to photograph another memorial service where she, Chiaki, and Ibuki perform in Koizumi's honor. Hajime also takes the moment to think about all those who have died so far — victims and killers alike.
Akane's happiness when Kazuichi gives her the miniature Mecha!Nekomaru toy. Made even sweeter that for the rest of Chapter 5 she carries him around with her, and he would at times shout out some phrases or words that correspond with whatever Akane is saying.
Monomi's speech at the end of Chapter 5 right before her and Chiaki Nanami's execution; in the midst of several characters' crises concerning talent, worth, and self-sacrifice, it's the sweetest and most uplifting case of Be Yourself.
Monomi: There’s no need to be a hero. You don't have to force yourself just to make people acknowledge you. When you do that, you end up blaming yourself, blaming other people...and feeling jealous of everyone... But still...it doesn't have to be like that. Even if people don't acknowledge you, you just have to be someone that you can be proud of! Cuz...you yourself are your biggest supporter! If you can learn to love yourself... That love will continue to support you for the rest of your life.
And an earlier, brief moment in Chapter is her response to Nagito's Self-Deprecation and very scathing self-descriptions. While the students don't ever seem to know how to react to them due to their rather justified mistrust and dislike of Nagito, Monomi is perhaps the only character in the game not to let the character's personality and cruelty get to her — she responds by earnestly insisting that the things they say about themselves aren't true and that no human being is trash.
When Monomi asks Chiaki where she got her kindness, Chiaki responds, "From my father, I guess...and my brother." The next chapter implies that this refers to Chihiro and Alter Ego.
Even more heartwarming: The English translation has her say "our dad and our big brother". Chiaki is confirming that Monomi is her sister in every sense of the word! Aww!
A bonus scene in the first chapter has more Heartwarming in Hindsight, as Chiaki invites Monomi to the girls' dessert-making party, and in the following CG they're sharing a plate in the background.
The fact Makoto used the 11037 number as a code to save the remaining students, the number which Sayaka Maizono, the first victim in Danganronpa, used to save Makoto from being framed as the culprit in the first trial. Makoto explained to Hajime that the reason he set 11037 as the code was because a certain person left that number behind to save him from trouble, proving that despite the fact Sayaka took advantage of Makoto's kindness and tried to frame him in the beginning, Makoto believed Kyoko's theory and remembered her dearly as a friend.
Not to mention that it's also a tribute to Leon Kuwata himself, since he was pushed into becoming the first murderer in the first game and seemed to get along okay with Makoto. Especially if the manga's turn of events was canonical and his fatal stabbing of Sayaka was actually completely accidental after all.
The whole simulation redemption plan is really sweet. Sure, Usami was really corny and saccharine, but in the pre-Monokuma part of the game she tries so hard to make the students feel safe, treat them with kindness, and encourage them to have fun and make friends. That's the worst Ultimate Hope has for his worst enemies.
It's even more heartwarming when you consider these are loyal followers of the person who forced him and 15 of his friends to kill each other, not to mention they're responsible for plenty of horrible things themselves during the Tragedy. Yet instead of letting them die or taking revenge himself, he instead chooses to give them a chance for a new start through the rehabilitation program. Even after everything he's been through, Makoto still believes the best in people.
As Gundam lays dying at the end of his execution, his hamsters watching, all of his departed pets descend from the sky and carry him into Heaven. An animal lover's faith in his pets is rewarded.
Made even more heartwarming by the fact that he thought he was going to hell.
In the Grape House in Chapter 4, you can see a statue of Sakura Ogami, though it is only labeled as "Ogre". Then you look at it and no one knows what or who it is supposed to be. This means that not only did the Future Foundation go out of their way to memorialize their dead friend in their rehabilitation program, but despite Monokuma vandalizing everything else on the islands (including turning Monomi's home into a haunted house), this statue alone is completely untouched.
Near the end of the game, Fuyuhiko says that Peko, despite being dead, was the one who inspired him to resist Junko's despair.
Fuyujiko: (smiling) In fact...I think it was the first time she ever yelled at me... Heh, I can't stand on my own two feet if she keeps treating me like a damn kid!
While this also doubles as a Tear Jerker, the fact that none of the survivors can bring themselves to hate Chiaki for being The Mole, with Sonia even insisting that Chiaki is still their friend.
Near the end of Chapter 6, Hajime is forced into a Sadistic Choice and goes into a Heroic B.S.O.D.. The person to break him out of it is the memory of Chiaki, who helps him move past his despair and stop playing Junko's game.
Best said with his final statement.
Makoto: Hajime...everyone...thank you.
Hajime: I'm not...the one you should be thanking.
Like in the previous game, the Island Mode endings often have characters coming to terms with their personal problems, especially when they weren't able to do so before they died. This includes Byakuya admitting to being the Ultimate Impostor and Peko deciding to help Fuyuhiko reach his goals as an equal, rather than a tool.
In Mikan's ending, Hajime promises to marry her in the future.
Peko's execution, in a tear jerking way. She resolutely tells Monokuma before it begins that she refuses to feel the kind of despair at dying that he so wants from her, and he responds by saying everyone gives in to despair in the last moments of their life and that she'll be no different. Nearing the end of her execution, she legitimately believes she's committed the worst crime a samurai can commit in slaying her master, which makes it seem like Monokuma was right as she cradles a badly-bleeding Fuyuhiko in tears. Then in the next chapter, Chiaki surmises from Fuyuhiko's injuries that Peko must have put everything she had into keeping him safe while her body was being torn apart. Even until the very end, Peko never gave up on fulfilling her duty, holding onto the hope that he'd be safe no matter how unlikely it seemed: she proved Monokuma wrong.
The whole notion that the six survivors of the original School Life of Mutual Killing ended up joining the Future Foundation. The Headmaster wanted them to go on to preserving hope for humanity's future, and against everything that Enoshima did trying to break that hope, that's exactly what they did.
The epilogue hints that not only did the survivors make it out of the Neo World Program with all their memories, but that their comatose friends could be revived as well. It's a small chance, but the possibility is there.
Sonia and Gundham's relationship, especially considering their pasts. Sonia lived a very sheltered life in Novoselic and never had a close friend, while Gundham is Not Good with People and has an easier time understanding animals. Both share an interest in the occult, with her asking to accompany him on a trip to an amusement park in hell. She's also the only person who manages to make him blush when complimenting his hamsters. Gundham refers to her as "the dark queen," saying she has great power yet to awaken. Considering this is Gundham, this is likely a massive compliment on his part. When Gundham is deemed the culprit in Chapter 4, Sonia refuses to believe it and even pleads with Monokuma to spare him, but Gundham convinces her to let go. His parting words about never giving up on life are also what inspire her to survive without any more killings.
The fact that Kazuichi of all people is the first person to legitimately suggest considering Monomi an ally in chapter 5, when up to that point every single character had constantly treated her as an enemy and an annoyance even as she put herself in danger to fight off the monobeasts keeping the students from opposing Monokuma.
Ibuki trying, in her own way, to help Hajime remember his talent. Even though he doesn't, she still encourages him to be happy with who he is, since, with or without one, he's still the same person she likes spending time with.
Similarly, in Chapter 5, Hajime has to explain that he was never a part of Hope's Peak's Primary Department, meaning that unlike everyone else, he doesn't have an Ultimate Talent. The reaction of the survivors could be summed up as "That's it? Who cares?".
Fuyuhiko: ...Is that all? Kazuichi: What. That's it? Dude, don't ever scare me like that. Chiaki: Cheer up, Hajime. It doesn't matter if you're from the Reserve Department. Sonia: She is right! No matter what, you are our friend!