There are quite a few. The first time one of The Many sneaks up behind you in System Shock Two and shouts "Look out!" or "Kill me!" is pretty bad. That game probably qualifies for creepiest, scariest and most disturbing thing in a game multiple times, a true horror classic.
Setting a zombie on fire in Half Life 2 is quite disturbing because its pretty obvious the person who has been infected is still alive enough to feel pain.
The Oceanside Hotel in Bloodlines is pretty scary as is Shalebridge Cradle in Thief 3.
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