Tops on my list that haven't been mentioned:
Full Meta Panic - Alternate future anime where the cold war never ended, lots of humor and dark moments in this anime.
Full metal alchemist brotherhood - If you like steampunky fantasy esque anime, this one will be great. Takes place in a world where alchemy instead of science rein supreme. Great storylines/character plots and conspiracy.
Noein - Trippy psychological alternate reality anime.
Bakemonogatari - If you like paranormal animes, this one is probably right up your alley.
Ghost in the Shell Stand Alone Complex - Cyberpunk dystopic future anime. Highly recommended
Endorsing Death Note, Kara no Kyoukai as others have mentioned.
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