Worst part?

[jaivyn]

Maybe weird, but the first part.. Archives, study etc. are much more scarier than the rest of the game for me, even after I finished it already.

[Amnesia15]

Storage & Dungeon is the scariest part for me :/

[Redeemer]

The funny thing about Storage is that by the time I had gotten there I had gained a sense of security that made me feel that if I followed my exploration procedures correctly I wouldn't run into trouble.

When I first entered Storage, you see, I didn't enter the small room on the left of the opening area, so I wasn't trapped by the monster right off the start. I actually explored the lower levels of the area pretty calmly, and it wasn't until I opened the room with the grunt hiding in it that I really lost my nerve. The surprise encounter at the top of the stairs didn't help things either.

So by the time I had left the Storage, I was glad I wouldn't have to go through it again, although I didn't start out feeling that way.

[Roy595]

For me, it was the Storage and Archives (not the one with the water monster).

Storage... for obvious reasons. The memento that said the darkness felt strange and unnatural was particularly unnerving. It was the first encounter with the enemy and there really didn't seem to be many good hiding places; it was a pretty open area. I felt genuine dread and terror and it took me a good month to crawl through this area.

It may be kind of weird but the Archives was pretty bad for me. The complete absence of people (and their bodies!) and that awful, droning sound really bothered me... plus the ominous monster noises and I REALLY didn't want to go down that hall with the piano and windows. Something felt very, very wrong in the Archives.

For some reason the prison wasn't that bad for me... I was actually having a good time exploring and taking in the atmosphere (then I had a hallucination with a flashing grunt chasing me and that freaked me out pretty good lol).

Tl;dr: Storage and Archives.