"Sorry, but your princess is in another castle" - truly disturbing.

ffvii: when your in the don's mansion and end up in the hottub witha buncha guys.
silent hill 2: when you walk down the endless stairs under the museum.
bible adventures: knocking out an eagle by throwing a chipmunk at it. (also most extreme moment in gaming) also,an inability to kill anything.
MGS1: fight with mantis or ninja
Resident evil 1: zombie eating the corpse on the floor in the beginning. (this was at the beginning of "Next gen" that scene alone was amazing.

Disturbing? I'm going to have to go with being chased by the guy wearing the pig mask in Manhunt. I dont know what the deal was with that part but i was absolutely fuckin terrified by this weirdo chasing me dressed up as that most delicious of culinary delights....bacon

That list stinks....

Ravenholm? Scary for about 5 mins, it just feels like an old fairground ride after that.

COD4.....WTF!!!!!!!!

Silent Hill 2....now we're talking, if the other games mess you up then a bit of SH2 will surely bring on some brown moments in those nice clean pants.

7th guest!!!!!!!!!!!!!!! AAAAAAAhhhhhhhhhhhh

Also...

Splatterhouse 2 on the genesis...My bloody god, cutting up mutilated babies with no skin with a chainsaw, a large floating mass of heads and blood and what not...

Remember playing that way back when I was about 5 lol, great days :(

Honestly, I thought Condemned was a lot scarier. That game created such paranoia at points that you were scared to move away from a corner because you just knew that something was going to come up behind you.

 I can believe that actually, hadn't thought of condemned it made me uncomfortable playing it on my own that I never got past the first bit where some drug addict nutter is round the corner, just not sure exactly which corner. Used to live on an isolated farm so those kinda games were never nice, in a good way.

on that SH2 scene: I found it to be quite pathetic actually.

The rattling locker in SH1 was much scarier.

Fatal Frame 2.

The blue filament suddenly turns red then your chased down to a narrow hall.

My most disturbing scene from a video game is the moment you encounter the the first Houdini-splicer.
You've just entered Arcadia, and you are exploring for a bit. But all the sudden, you see a splicer walk around a corner. You follow him, but nothing's there. You proceed.
Then you see the splicer again, walking past a pillar... but when he should reach the other end of the pillar, there's no splicer....
Anyway, you move on to finally reach some desk with a wooden bunny-mask on it, a mask just like the one the splicer was wearing. Then you hear the splicer talking from very close, you turn around... ZOMG HES STANDING RIGHT BEHIND ME!!!1!!!!!!

Another quite disturbing moment from that game is Fort Frolic. The sadistic artist who forces some guy to play piano or else he'll blow him up... when he does, you're supposed to take a photograph of it and put it on his masterpiece, made out of people trapped in plaster, like mummies... in plaster. Then you have to find some other guys, kills them, take a picture, and put the picture in the masterpiece. While looking for the other guys, you come across some more compositions made of plastered people, in all kinds of creepy poses.

The disturbingness of this level is so great, and it goes hand-in-hand with the outstanding gameplay of the level.

Once I completed the masterpiece, and the artist showed up, I decided not to kill him, out of sheer thanks for the great gameplay experience he gave me. Bravo!