Hiyoko, who is a pain in the ass to pretty much everyone sets up a memorial for Koizumi after the latter has been murdered.
Akane's happiness when Souda gives her the miniature Mecha!Nidai 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 become a hero. It’s okay to not need to be considered worthy by someone else. That causes you to blame yourself and blame other people…and because of that, become jealous of some other people…but you know…that’s not the way it is. Even if no one else considers you worthy, it’s okay to just become someone who can be proud of yourself! That’s because…you yourself are your biggest supporter! If you can come to like 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 Komaeda'sSelf-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 Komaeda, 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 Nanami where she got her kindness, Nanami responds, "From my father, I guess...and my brother." The next chapter implies that this refers to Chihiro and Alter Ego.
The fact Naegi 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 Naegi from being framed as the culprit in the first trial. Naegi explained to Hinata 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 Maizono took advantage of Naegi's kindness and tried to frame him in the beginning, Naegi believed Kirigiri's theory and remembered her dearly as a friend.
Not to mention that it's also a tribue to Leon Kuwata himself, since he was pushed into becoming the first murderer in the first game and seemed to get along okay with Naegi. Especially if the manga's turn of events were canonical and his fatal stabbing of Maizono was actually completely accidental after all.
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 Muscat house in chapter 4 you can see a statue of Sakura Ogami, though it is only addressed as "Ogre" when 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, Kuzuryuu says that Pekoyama despite being dead, was the one who inspired him to resist Enoshima's despair.
Kuzuryuu: (smiling) Now that I think about it, I guess it's the first time she's ever scolded me. Heh, how long does she think I'm going to let her treat me like a kid?