You guys have already mentioned a lot of the films I would have, so I'll just try to add a few:

Contact - What can be said...beautiful, remarkable, wonderful. This is what happens when genius meets genius.

Signs - Sure, mediocre science fiction at best, but then I don't consider it a science fiction film.

Bringing Up Baby - pinnacle of the screwball comedy (tied with What's Up Doc)

Miller's Crossing - the Coen brothers are as adept with drama as they are with comedy (as in Raising Arizona)

Star Trek:First Contact - another pinnacle, imho. High water mark of the ST franchise.

Koyaanisqatsi - Mesmerizing. The director said something to the effect that he wanted to make a feature film where actors have been removed and location takes over. Goes far, far beyond that, though.

Mystery Men - though I really got a kick out of Spiderman 1 & 2, and XMen 1 & 2, Mystery Men is maybe my favorite superhero movie. If there really were superheros, I bet this is what it'd be like.

Groundhog Day - rivals Chinatown and Back to the Future as possibly Hollywood's Greatest script.

Glory - Friggin depressing, which I suppose a war movie should be.

Dogma - I don't think there's any end to how brilliant this one is.

To echo recommendations made by others: anything by Miyazaki, but especially his latest work (Spirited Away, Howl's Moving Castle). I'm a HUGE fan of cgi, but Miyazaki's work is just totally breathtaking. Also: Apollo 13, Forbidden Planet, Vertigo, Ed Wood (which is a fairly accurate depiction of what low-budget movie-making is often like), Alien/Aliens.

Guilty pleasures: Jurassic Park (any of 'em), Galaxy Quest, Cronenberg's The Fly, Carpenter's The Thing, Mouse Hunt, Final Fantasy, Die Hard, Ocean's Eleven, Terminator 2, any of the Star Wars movies.

Sorry about that, I went a little overboard...and still didn't get to them all, not by a long shot.