I'd say Amnesia: Dark Descent. The inability to really fight back made it much scarier to me. That's the problem with many near-great horror games; they might have wonderful atmosphere and design and plot, but ultimately if I feel I can fight your creepy monster and survive, it's not going to scare me. Dead Space 1 is the poster child, in my mind. It's also why pre-RE4 RE games were scary... the controls were so clunky you might actually die. A flaw HELPED that game series.
I will agree Condemned: Criminal Origins also scared me quite a bit when I first played it. Something about the atmosphere really worked.
Honorable mention to Alan Wake, whose creepy forest and focus on unsettling rather than jump scaring went a looong way. --- "Life is like a box of chocolates. Diabetics can't enjoy either."
Fatal Frame 2 Crimson Butterfly Directors Cut Edition on Xbox...never even finished the game man...stupid house of haunted dolls and specters... --- --- I'd never dream of invading M'ladys privacy while the Duke invades M'ladys privates! ---
Eternal Darkness, especially the moment when you are told your memory card is corrupted. I wish I had a photo of my face the first time I saw that :P --- "My game won't let me buy a girlfriend." - GamersTavern The official Mareep of the pokemon X and Y boards.