Damn I hated that part of the game. I would get so frustrated that I thought to myself "When I find this baby, I'm going to kill it then he'll shut up"

yeahhhhhh

SPOILER

but there was also a sort of "huge spider walking" noise in the big room at the end of the prison, I looked everywhere to find it

That scared the shit out of me!

The Silent Hill franchise has freaked me out a lot with the fantastic sound design.

Resident Evil 4 was pretty scary, but the thing that scared me the most were those regenerators. And I hated (loved) the sound they made, so scary.

The entirety of Eternal Darkness.

the water creaky noises in bioshock :X not that scary, i know. but so deep under the water, you know if the glass breaks you're done for >.

also, sirens in any game (and real life) are scary. and those redead in OoT, too.

*makes mental note to play more scary games*

Eternal darkness is probably the game with the scariest sounds. Silent hill series are second place. Doom, resident evil, max payne when max was dreaming, bioshock is all i can remember now.

Nemesis yelling S.T.A.R.S, regenerators from RE4, the children laughter from Clocktower 2 and as somebody mentioned the Alien radar sound... I never was scared from SIlent Hill... I dunno why :-S

for me the sounds in fatal frame 2

I agree with you on the reaper's chains in Persona 3.

There is also the sound of that monster walking in the cancelled game Winter. Go at 3:10.