It's a bit of a Guide Dang It to trigger, but in Chapter 4, a secret scene involves Naomi breaking down due to Seiko's death...only for Seiko's ghost to appear and comfort her. Seiko assures her that she will always be with her in spirit, and asks only one thing from Naomi; a kiss.
At the end, Naomi discovers that she was the one who killed Seiko while being controlled. How on earth does she not immediately succumb to the darkening, you ask? Well, at the very end, when she admits what she learned out to Satoshi, we find out: As Naomi was falling into the depths of despair, she received a text from Seiko. The same text Seiko intended to send to Naomi before she died, apologizing for their fight. Naomi didn't understand why she got the text at that moment, nor did she care, convinced that Seiko died hating her. She receives the same text a second and third time. Naomi initially thought that Seiko was spamming her out of spite, until she realized that the text was titled "No hard feelings". It's enough to bring both Naomi (and the player!) to tears.
The song that starts playing in the background as Seiko's texts start piling up doesn't help the waterworks at all.
Although some people find it Squicky, the "Extra Ending" of Chapter 5 where Yuka admits that she loves her brother is touching in its own way. Even though she knows that Satoshi doesn't return her feelings, she still willingly Takes The Scissors that are intended for him.
It's rather sweet watching Mayu and Nana bond over both being in the drama club after Mayu and Yoshiki save Nana's life.
In fact, simply having a scene where our characters are actually able to save someone at all. Remember, in the first game, most of the other people you encounter are either too far gone to be reasoned with, and/or trying to kill you.
Kishinuma saving Ayumi from being possessed in Chapter 2 of Book of Shadows. Extra points for finishing his speech by hugging her.
Although it's a Wrong End, in Chapter Five if Yoshiki refuses to return to Heavenly Host with Ayumi he and she have a very heated argument which leads to Yoshiki confessing his love for Ayumi and being happy that he got to spend the time together with her alone so she could look at him for once. He also reveals his jealousy and insecurity over Ayumi being infatuated (and possibly slightly obsessed) with Satoshi, claiming Ayumi only wants to go back for him and not the others. She, however, denies this and says that she does in fact want to have her friends back and to be able share happy moments with all of them again. She even admits that she's deathly afraid of returning, but she'll do it anyway. This results in Yoshiki breaking down into tears and sobbing, seeing hallucinations of his comrades and ultimately leading him to begging Yuki to take him too. It's thought by fans to be one of the most powerful scenes in the whole game and think it should've been included into the game's canon plot-line; considering its wonderful Character Development for Yoshiki and the voice actor's emotional and heartwarming performances really selling the thing.
The ending of Yui's flashback during the Encounter chapter of Book of Shadows is very sweet even with the knowledge that Yui and Tsukasa are apart in the present. It's a very nice scene despite how anti-climatic it seemed to be in the first game.
At one point in the game it's possible to find a pair of skeletons holding hands, with a note left behind that as long as they have each other death doesn't frighten them, and that their loved ones shouldn't worry or miss them. Considering how the school is set up it's possible that if they really died full of love then they'll be experiencing it forever.
Naomi's reaction to waking up after being saved from death by hanging and finding Satoshi tending to her is to hug him and bawl on his shoulders. Even moreso if choosing the "There's no need to apologize..." option after she realizes what she was doing.