I don't take cartoonishly evil villains seriously. The best villains may do bad things, but they typically mean well and their side may be well argued enough to make you wonder if things would be so bad if they won. The Zeon come close to being an example, but all they do is drop colonies on things and wipe out most of the human population, including the people they are supposedly trying to free. So close, but the Federation makes you look like assholes because that's what you are.
EDIT:
It's wierd, but for some reason one of my favourite villains is the Dr. Eggman of Sonic X and the SA games. He is evil, but when push comes to shove he'll willingly clean up his own messes, and he approaches the whole "fighting good" thing a lot like a game.
Absolute favourite villan though: Palpatine and the Sith. Seriously, what's so great about the Jedi? They don't make anything better or different and they've torn the galaxy apart in their retarded little wars at least twice.
EDIT:
It's wierd, but for some reason one of my favourite villains is the Dr. Eggman of Sonic X and the SA games. He is evil, but when push comes to shove he'll willingly clean up his own messes, and he approaches the whole "fighting good" thing a lot like a game.
Absolute favourite villan though: Palpatine and the Sith. Seriously, what's so great about the Jedi? They don't make anything better or different and they've torn the galaxy apart in their retarded little wars at least twice.