I am always amazed when I come into threads like this and see the FEAR games mentioned. There are a few really pathetic jump scares, unscripted ghostly apparitions and objects moving around which I usually missed because I was LOOKING THE WRONG WAY.
On my list of scary games Fear comes somewhere under Ravenholm from HL2 and that's pretty far down.
Amnesia
Outlast (little blunt but good)
Penumbra
Cry of Fear (mod)
Condemned
Dead Space 1, mainly atmosphere (hur hur)
Stalker Series has its moments, again mainly atmosphere
Those are the only vaguely modern games I would look at really, horror hasn't been very popular over the last 10 or so years.