My favorite battle is against is Miror B. His music is the best music I've ever heard in a Pokemon game, the only other music that really even compares is the Cipher Admin. music IMO.
My toughest battle was against Ardos, stupid Swellow and it's accursed Spd. and Shadow Break, I had too kill the thing just thing to stay alive, but atleast that means I get hear the Miror B. music again.
Miror B. because he was the one that inspired me to dance. Basically, I like all of the Cipher Admins and standout bosses considering these guys actually had some personality compared to the ingame handheld bosses, which went straight to the battle and made me think they were all mindless drones. Battling these guys in actual challenging matches inspired me to write a lot of fanfictions, and I hope Diamond and Pearl gives more life to the game bosses.