I'd have to put Haibane Renmei (English: Charcoal Feathers Federation) way up on my list, for everything about it was absolutely beautiful.
Witch Hunter Robin was slow-moving to start, but it had a range of emotion not commonly seen in anime, and a development of character that was amazing to watch unfold.
Hoshi no Koe (English: Voices of a Distant Star) was just... It's the only anime that ever actually made me cry. Makoto Shinkai is absolutely brilliant. His other works (5 Centimeters per Second, The Place Promised in Our Early Days) along with his short animes (She and Her Cat, Tooi Sekai (English: Other Worlds)), were amazing as well.
I'm not sure what it is about Full Metal Panic that I love so much, but there you have it.
And last for this list (but not least of the list, either; I'm not going in a particular order) would be Pale Cocoon. The colouring is wonderful, the situation believable no matter how deeply rooted it is in science fiction, and the music breath-taking at points. For a wonder, it also has an environmental message. It's a must-watch short film for anyone.