Alien vs Predator games were really quite scary to me, not so much because of the atmosphere, which could have been done better, or the graphics, which although good weren't draw-dropping. But it was that motion detector.
Walking down a dark corridor, getting a single ping, stopping dead, then the ping doesn't come up on the next sweep. Waiting again and hoping it turns up again before you go forward...then eventually having to go forward, knowing that there's something there in the darkness waiting. The way that thing worked was seriously brilliant, it scared the daylights out of me.
Silent Hill 2 had something similar, that little radio that emitted the static as you got closer to an enemy. The all encompassing fog and how you weren't Superman with an arsenal of weapons that a small country would admire also really added to it.
I've never been into Resident Evils, and I didn't think Resident Evil 4 was even all that scary, with the glaring exception where (spoilers) you play as Ashley. When you're playing as Leon you have a huge arsenal at your disposal, your array of handguns, shotguns, rifles, and even the grenade launcher and RPG. As Ashley, you have nothing except that flashlight, and when the walking armor suits pursue you with that distinct clanging noise getting ever louder, it gets really intense.