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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Grew up with Adult Swim/Toonami here: Rurouni Kenshin Cowboy Bebop Trigun Yu-Yu Hakusho Inuyasha, etc. etc. and also- Samurai Champloo Get Backers Weiss Kruez Tiger & Bunny.... Oh wait I was only supposed to list one lol.