I would have to say my all time favorite is Eureka 7, followed by Clannad. What's yours?
edit 1: holy crap over 1000 replies! I see we have tons of otakus here. Haha! Keep it up!
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1) Parasyte: The Maxim 2) FMA Brotherhood 3) Steins;Gate 4) Princess Mononoke 5) Future Diary