The discovery of Natre's decomposing corpse. The Jump Scare is fairly easy to see coming, but still manages to be horribly jarring.
Tun's nightmare in which he finds Jane sitting alone in a classroom, coughing up blood and spitting out her own teeth.
After a photography session, Tun is alone in the room when the lights start to flicker... before going out completely. Now, imagine yourself in a pitch-black room, with the only light source being the flash of the camera that has suddenly started operating by itself... and you swear you can see someone advancing on you in the brief flashes of light...
The night time "chase" sequence in the apartment. The entire scene.
Megumi and Natre's rape is also very horrifying. The act itself is already very despicable, but imagine the despair the girl must have felt when her boyfriend was right there in the room and wouldn't even lift a finger to save her.