Tough choice.
Trigun, Cowboy Bebop, Black Lagoon, Fullmetal Alchemist: Brotherhood, Hellsing: Ultimate, and Stein's;Gate are all tied for my favorite.
I can't decide.
I can tell you my top two favorite mangas, without question:
Berserk.
Vagabond.
But the Berserk animes are disappointing...