Of all time:
Mugen from Samurai Champloo (my favorite anime, also). Because he's probably everything I could ask for in a character. A dude who just doesn't give a fuck, he can breakdance, and kick ass usually barehanded at anytime. Despite the fact that he was illiterate for the majority of the series, he was just bad ass, and he had a troubled past, survived being shot something like four or five times, and I could keep going. Mugen. Badass. The best of all time.
I'm also a fan of:
Spike Spiegel from Cowboy Bebop
Kenpachi Zaraki from Bleach (aka, the reason to watch the show)
Alexander "The Paladin" Anderson from Hellsing
Gene Starwind and Harry McDougal from Outlaw Star
Holland from Eureka 7
Greed and Maes Hughes from Fullmetal Alchemist
Rock Lee, Kisame Hogashi, Shikamaru Nara and Hidan from Naruto (even though I only read it, because the show is a load of steaming horse shit)