The main cast's backstories, especially Takuru, Hinae, Nono, and Uki.
The scene where Takuru and Nono retrieve Uki from the hospital. First, they foil the plot by Kunosato and Shinjo to basically kidnap her, then find her in the basement in the midst of a Heroic BSoD because everyone she took care of has vanished without a trace and she is at a complete loss. Nono can only hug and cry with her until she finally calms down. It turns Heartwarming when Nono tells her, "Let's go home," and they take her with them to Aoba Dorm to become part of the family.
Nono: You really... hung in there, huh? But it's okay now. So let's go home, okay?
Both of Uki's good endings. One has her be a vegetable and cared for by Takuru, and the other has her flat-out die. Takuru is also suffering hallucinations from her death, as seen in the CG where it shows her shadow standing in a doorway.
Everything about Yui's death, but especially after The Reveal. The poor girl, who had problems with trusting men, was murdered and cut up by her brother's best friend, who was being mind-controlled and manipulated by her brother's childhood friend and her foster father. Nono’s reaction and subsequent breakdown in mournful wails is all too real.
Nono's death in the common route, especially when Takuru returns to a First-Name Basis with her... right after she passes away.
Hinae's mother telling her daughter how she always hated her and wished she were dead. Hinae being a Living Lie Detector only makes it worse.
Megumi: "When you were born, it ruined my life!"
Tottaly true.
Megumi: "I never should've had you! Or Shingo! A creepy girl like you... You never should have been born!"
