Yama Ishimoto in general. He starts out as being somewhat unlikable. Then you find out just why he acted the way he did. He lost his sister at a young age, his best friend left causing him to go into a Heroic BSoD that nearly ends in him committing suicide, and he still feels totally inadequate. Yama really needs a hug!
Along those lines, all of the character trailers. They all start out somewhat positive, only to do a complete 180-degree turn down depressing town.
Among the main heroines, arguably no one has it worse than Airi. Not only are both of her parents dead, but her quiet and aloof personality makes her a target of severe bullying by her classmates. This only gets worse following the student murders, where Airi is outright accused of the disappearances, whether directly or indirectly, despite a clear lack of evidence. Even after some strict lectures from Mr. Ryouta and the principal, she's still being relentlessly harassed, and its implied that she's still facing stigma even after the identity of the true murderer was revealed. It's even suggested that Yama and Rui are the first people to ever stand up for her. Needless to say, she's been through a lot
Yama and Rui's fight. You really feel for both sides. You feel for Yama because you can see just how much he absolutely loathes himself, and you feel for Rui because she is just absolutely broken by Yama's harsh words. It takes the two a while before the animosity is lifted between them.
The bad endings. They all end with Rui and/or two other students getting murdered, and this really pushes Yama's Berserk Button causing him to lash out at the killer in vengeance.
The good/true ending has a few of these. Namely...
Yama's inner monologue about growing up in an alternate reality where he was able to live on his own without relying on others. It's bittersweet because it marks the beginning of his journey towards self-acceptance, but it still shows that he still has some feelings of inadequacy.
When Yama visits Mizu's grave. He tells Mizu that he's finally ready to accept himself and move on with his life. Doubles as an absolute crowning moment of awesome. Triples as a heartwarming scene.
Seeing Yama and Rui patch things up. It's not going to make everyone cry, but it does fill one with the warm fuzzies.
Rui's death. How does this scene break the heart. Let us count the ways...
All of the bad endings, while dark and depressing, at least gave the benefit of hiding Rui's body. The good/true ending show's her body in all of it's gut-wrenching glory. Her eyes are completely open and her expression is absolutely soul-crushing!
Yama's inner monologue leading up to the discovery. "Maybe she escaped while her parents died and..." NO! Do not go there!
On a less depressing note, many Precision F-Strikes were probably had when that happened. It comes out of nowhere right after an hour-long epilogue of Yama and his friends reuniting and hanging out happily despite the incident causing a stir in their lives. Yama exchanges what seems to be his (platonic) final words with a girl of his choice, and everything seems like it's about to end as he makes his way to Rui's house. When the text describes her parents' corpses, the player may realize what this likely means for Rui's fate, but refuse to believe it could happen. Then, Yama looks under the kitchen cabinet, and everything comes crashing down.
". Make. It. Stop!