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.
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 the reason he set 11037 as the code 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 were 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.
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 BSOD. 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.
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 Imposter and Peko deciding to help Fuyuhiko reach his goals as an equal, rather than a tool.