I'm going to be a little obvious in some of these; but I think #1 will surprise quite a few.
5) Clock Tower 3.
The game could have ended after the first boss, and I would have been thrilled. The first boss makes such an impression, everything else was disappointing in comparasion
4) Medal of Honor Underground.
This game gets very creepy and quite graphic (well, as graphic as PS1 could go, at the time) the further into the game you go. It is an extremely long game, and after your done, you can play through as the female spy. I don't think my husband ever finished it. I loved watching him play just so I could follow the storyline. Dobermans that can shoot M-16's while you are trying to find a scientist's scattered remains is quite creepy indeed.
3) Silent Hill.
The original is still the most brutal. I seriously debated putting '2' in my list; but, quite frankly, it never scared me or creeped me out. its a wonderful psychological thriller and a fun game to play, but scary? Not so much. I think what puts 1 over all the SH titles is how unforgiving and how fragile human life is in the game.
2) Fatal Frame.
Yet again, the first is the best. You can't fight a ghost; but you can sure shutter them into oblivion with an archaic camera. The graphics are beautiful, the atmosphere is tight, and you always feel like you are probably missing something, but you don't know what until its too late. The storyline seems random; but as the nights pass (there are 4 levels to the game, you survive a level, you've made it through the night) you see how terrible and mysterious the mansion grounds are. I can't give this game enough praise.
1) Sanitarium.
This is probably a pretty obscure title to most, around 10+ years old, and sadly, I've not seen anyone make an updated version of it. It was a point and click PC game with a very in-depth storyline. It begins with an arrogant doctor who, while driving from the sanitarium he works at, crashes off of a rain-slicked road. When he comes to, his injuries have been tended to, but he finds he has been left alone with all the other criminally insane in the sanitarium. Through his dealings with the other characters, he finds just as much out about himself as he does the patients he is helping along the way. I wish like hell I knew how it ended, but my friend I was playing the game with moved and lost that, and a few other games in transit. It does fall under the label 'psychological thriller' like SH2; but unlike SH2, the game deals alot in the abstract and visually disturbing.