The first (and the best) Alone in the Dark have a few spooky sections. Right from the beginning I might add ;)

Something that really made me jump out of my chair was when you enter that underground bunker in the first S.T.A.L.K.E.R and hear a loud groan..

The first Penumbra is also one that quickly made me slam the Esc-key. I'd say that's hands down the spookiest game I've played.

Upvoted.

The same two immediately came to mind as missing when I read the top 5.

Press F to outrun the monster

First 'scary' game for me was playing the Silent Hill demo on ps1; game rocked my world and I went on to also check out this 'resident evil.'

System Shock has to be mentioned on this list as well. Atmosphere is spot on!

Deadspace (1)

They were scary in Doom 1 and 2 too.
I once watched my old gaming buddy play. Being a bit distracted by me he opened a door and thought the room was empty. When he suddenly saw the pinky he jumped half a meter up from his seat.
Never knew he was that athletic.

My cousin nearly had a heart attack with that pinky. The moment it burst through the glass after failing to break through the door, he jumped up in his chair and started throwing grenades everywhere, the result of which was that he killed both himself and the pinky :D.

They are scary in Doom 1&2 especially if you turn on -fast monsters :P.

I think games like Amnesia and Silent Hill don't fit the list because they don't have a specific "scary moment" which is what that list was about. It deserves the clarification of what scary means versus terrifying.

When the dogs jump through the windows in Resident Evil your first time playing, that's scary, a jump scare.

When you walk through a dark, abandoned elementary school and hear a baby/dog(?) sound, that's terrifying; nothing particularly scary about that sound or setting, but the atmosphere makes it very disturbing.

Though I would probably say the point in the school when you pick up the phone and hear your daughter begging for you to save her as one of the most intense and frightening moments I've had in a game. I love SH2 as well, but it's atmosphere is more depressing than horrifying compared to the original or even the third.

Honorable mentions to My Lovely Daughter for the first time you must sacrifice one of your beloved children. Great design to make you fear what you are capable of rather than death or harm to yourself.

Discussions like this highlight exactly how often people forget that Doom is as much horror as it is action. Or at least, it was.

Not a horror game, but there's a plot point in Crusaders of Might & Magic with the Crusade soldiers that is revealed in a very startling visual way. It raised the hair on the back of my neck. I recall trying to move the character forward to get a closer look and being unable for a long moment.

Nah I can't even remember that FEAR scene. The scariest one was where Alma dashed out from under a table after nobody else was left and then just disappear right in front of you again.

I haven't played this game since around the time it came out. I distinctly remember a moment when you turn to climb down a ladder, and Alma is standing in the exact spot you just were.