A lot of my top picks have already been mentioned -- The Thing, [REC], and The Exorcist are the three scariest movies I've ever seen. The Orphanage is also very good, though more of a drama (and an effective one at that), with a few very well staged creepy scenes.
A few more to add:
- It's sort of hit or miss, but John Carpenter's In the Mouth of Madness really worked for me. Before [REC], it was the last movie that made me turn on all of the lights. It's a bit ridiculous, and doesn't quite work for everyone, but its worth checking out.
- Most people have seen Shaun of the Dead (if you haven't, you should!), but James Gunn's Slither gets overlooked. I think it's just as good when it comes to mixing scares, gore, humor, and genuine pathos. The performances by Michael Rooker, Nathan Fillion, and Elizabeth Banks are excellent, and the Bloodshot records soundtrack rocks.
- To go along with the other French movies mentioned, I really liked a movie called Malefique from a few years back. It's a pretty bizarre movie, more so than actually scary, but effectively so. The director, Eric Valette went on to direct the crappy American remake One Missed Call, but don't hold that against him.
- Speaking of bizarre, a Japanese movie called Suicide Club is the single weirdest thing I've ever seen. No narrative cohesion whatsoever, but worth watching.
- A few classics: Eyes Without a Face (also French) has some great disturbing visuals, as does an older American flick called Carnival of Souls.
- A few others that are well-known, but people should see if they haven't: Evil Dead II, The Host, A Nightmare on Elm Street, the first three Romero Dead movies, early Cronnenberg, Poltergeist, Susperia, An American Werewolf in London.
- A few episodes of the Masters of Horror series are worth checking out, particularly Carpenter's "Cigarette Burns" and Landis's "Family."