These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Some would put it a little later, when Fuminori brutally rapes Yoh. It's not his first heinous act, but the ones before that (breaking Yoh's heart, going along with cannibalism, and attempting to murder Kouji) were in direct response to the really bad hand life had dealt him. Raping Yoh, though, that's pure sadism.
Paranoia Fuel: While the game exaggerates its effects, Agnosia is a real disorder that, due to brain injury or neurological trauma, can distort a person's senses and perception in many different ways. Eep.
Tear Jerker: The whole damn game, really. The music contributes a great deal to this.
The Woobie: Yoh is the most obvious example, although a case could be made for pretty much every character in the novel. Yes, even Saya.
Yousuke. Has a loving wife and a daughter, and paints in his spare time. He's practically the ideal family man. All seems right and blissful with his life... until Saya comes in.
Kouji. He just wants to help his friend become normal again and he pretty much saved the world in one of the endings. His thanks? His friends are dead and he can't sleep knowing there's more of Saya out there somewhere.