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."