Number one rank is really easy for me.
Penumbra Black Plague with novint Falcon force feedback controller
Penumbra Overture with novint Falcon force feedback controller close second.
Black Plague wins because they dared to not show the ghost and then actually make the damn thing immortal. You couldn´t win!
I am sure this are solid horror games in their own right but having a physical connection to all the objects and wall. You can feel the texture and contours and feel the weight of things you lift off. The novint controller is so precise you just can´t help to buy the illusion even further then you normally do. Very special.
I am not very skittish but at one point I was truly paralyzed in terror at Black Plague totally unable to defend my character had I been detected. And I thought I was battle hardened at that time with Doom, Alien and what not. The original alien never did scare me this much!
I haven´t played Amnesia partly in frustration that they don´t have any cooperation with novint anymore. I tried a few hours but it´s just not the same with mouse/keyboard. I guess it´s the thing of been there done that. The really good scare don´t work for sequels generally. Black Plague the exception.
System Shock 2. Very thick atmosphere and really tough survival on harder difficulties. I remember it as amazing in every way haven´t replayed it though but played it some years after it´s initial release.
Shalebridge Cradle level in Thief 3. This level is so brilliant I want to take it on even if Thief 3 is not all that terrifying. Overall I would probably want to pick perhaps Thief 2.
Alien vs Predator the original. Got it via Sega power pack on the summer sale and it´s not quite as scary today as it used to. I am of course generally talking about the marine campaign. Remember particularly a level on a dark knight outside in a sandstorm with tons of containers making your motion detector beeping all over the place. I tried to replay that some years later from my first play through but when I got there I just gave up. I won´t do this :D
Honoury mentions to Silent Hill 2 and Resident Evil 2 and parts of F.E.A.R