FEAR 1 was good, and a number of other games had good moments of suspense or fright, even the Half-Life ones to some extent, but the number one most scary game I ever played, and this one actually made my heart race with adrenaline and jump as I was attacked (I think I even had a dream or two way back about it) was AvP (the original). Specifically, it was AvP playing the Marine campaign.
Something about the atmosphere, knowing what the bugs could do, losing night vision when you wanted the motion detector and vice versa, having almost NO save points! (I think lack of save points was annoying at first then when I got used to it after the first mission, it really added to the sense of urgency, the motivation to stay alive...)
Doom3 tried, but bless its heart I was just never scared. Not like AvP scared me.