Ok, I had to register to add some ideas here......one of the scariest mods I've ever played was called Affraid of Monster, for HL1. (will post a link if anyone wants me too, otherwise just google it).
Several occasions I turned a dark corner, to suddenly find I'm instantly being attacked by a zombie....from behind!
Also....invisible zombies...nuff said..lol
Anyways....you can get loads of ideas from that mod if you get stuck....heres some of my own.
Atmosphere.....this is important...if you can use sound fx, speach and music subtly in the background...that always helps....people usually overlook music...but just think of the best horror films and how the music kicks in before and after the fright!
I like the bit in nightmare house where you where following crying (I think it was anyway)....that helped with the atmosphere alot!!
Imagination is the scariest bit...never fill in all the details...either darkness (obviouse)...or full lighting and something you can't quite make out/blurred (not sure anyones tried that before)
Instead of a person being dragged into a vent.....how about having equipment (healthkit when low on health....or a more powerful gun) dragged away from you (into a vent....or down a coridor with a child laughing....perhaps with a trail of blood behind it)
Don't think anyones done that before!!
Dream sequences...I know they've been mentioned...but there are other ways of doing them....they can be more subtle (buffy the vampire slayer did good dream sequences. Battle star galatica is doing some good ones too)....make the player think it is reality but just start bluring the lines....
Slow down movement.....make walls or doors crumble as unseen forces try and get through...have things disapear and reapper.....or flash in and out like you did with the stalkers.....perhaps make it a slower fade though?
Floor falling away....or pushing up....stairs....now that a good one, have it turn into a slope and and slide the player into a room full of zombies.
Make everything seem fine, then put the player back into the game
Last but not least.....people (or corpses)....blank staring people work best....one person floating in the middle of the room (not dead)...bit like the women in nightmare house with the noose...
Or perhaps a room full of people just staring at you....or just staring into space not moving......the lighting could get brighter and brighter then flash....the room comes back into focus only to find the rooms now covered in blood, no people...and sobbing can be heard.....only to have the lights then fade out to black, scream or heavy breathing and the room now fill with zombies....as the lights fade back in slowly
Hope that helps!