Let's see...I believe the other thread was just "scary games in general," but this one is actually asking for scary moments. In Resident Evil 1 when the dogs jump through the window, of course. I honestly couldn't pick it up for a year after that. I actually beat it later on though.
Resident Evil 2, when the Neo-Tyrant bursts through the wall right after you're walking back down the hall towards the camera. Scared the FUCK out of me. Hmm...in Silent Hill 1, anytime during the school or hospital. Those that have played it know the horror.
In Eternal Darkness for Gamecube, just about that entire game had me on my nerves end. Except for when you get the Elephant Gun with Nitro Slugs a little after half-way through the game with that one character. I could kill anything with it so it made it seem a *bit* less scary. A few noticable scary moments were checking the bathtub with Alex in the second floor of the mansion and the first time I heard knockings coming from the other sides of doors in the mansion. Then you go through and nothing is there. Then you walk back through and your head explodes, game over. Ha ha, then the game would pop back up to right before you went through the door in the first place. My hands were shaking the entire time the Sanity meter was low; expect WEIRD shit to happen when it is. Fucking screams coming from everywhere, people screaming to "get them out of here," and the blood dripping from the ceilings just creeped the fuck out of me. I had to play for short periods of time or I simply couldn't go on. Now that I think about it, Eternal Darkess is easily on par with Silent Hill on the creep-out psycho-shit factor.
-Lasereth