The nightmare sequence right at the beginning. Some people, such as Brad from 4pp, refused to play the game after the nightmare.
It doesn't get any better with later nightmare sequences, either. Especially the one where the Facehead from the first nightmare reappears, as well as the final ones.
The pedophile in the apartments of the first chapter. He was not content with raping children and killing them, but also found a liking to eating them. He even rendered the building´s elevator non-functional, so that the kids would have to take the stairs, where he would be waiting, and pull them into his apartment.
Once the player explores his apartment he discovers a room full of photographs of the victims killed, slaughtered in different ways on all the rooms walls. Then the player gets locked in and the lights go out...
The Sawrunner. He can't be killed and chases you at a insanely fast speed. If that isn't enough he moves in a freakish way and has a terrible scream which will send a shiver down your spine. You'll be paranoid for the rest of the game, as he likes to suddenly appear and cause a chase sequence.
Migitated by the fact that, at least on Easy and Medium difficulties, you don't even have to sprint to avoid his One-Hit Kill attacks; he pauses each time he does a swing, allowing you to slog along at the normal pace as long as you don't stop at all. On Difficult and Nightmare, however...
"Watch out for the trees". Yes, you better do.
Since basic enemies can sneak up on the player without making a sound, jumpscares are abundant.
The school. Initially, it is well lit and abandoned, lulling the player into a false sense of monster-free security. However, the shit hits the fan when you tinker with a fuse box in one of the rooms, with bloody monsters around every corner in the now darkened halls. The worse part: the school is like a maze in the dark, with desks cluttering the floor and multiple classrooms you can access.