Sky Crawlers, it essentially challenges all the otaku criteria that feature heavily in today's anime. It is dialogue-intensive so don't expect an action-packed thrillfest.
The Girl Who Leapt Through Time.. Lovely pinch of fantasy that is not getting its due attention. Ponyo is nice and all but it's basically the same rehashed Ghibli Studio formula.
This series is a bit older but it's already one of the finest ever. From THEM Anime Reviews - "One of the best shows I’ve seen in a while, Planetes is an excellent and engaging work that while addressing a number of thematic issues, never loses its character focus. If you absolutely positively must have high-end action in every episode, you might want to subtract a star. If you like your anime completely free of political or philosophical exploration, you might want to subtract a star. Everybody else, enjoy! — Jeremy A Beard"
Paranoia Agent is an excellent show that mixes surrealism with psychological thrills (I hope I got it right!). Its conclusion is a bit iffy for some but I liked it.