Ultron Undying!!!!
At the moment...
Ultimate Venom. I'm a big time Spider-Man fan and picking a favourite has become really tough because you've got both Incarnations of Carnage (KILL KILL KILL), The Original Green Goblin but with Miles Morales, Venom has become unstoppably evil and twisted (reminds me kind of like Doomsday).
Thanos
Others who come close:
Doom
Void
Ultron
Tough question. On a different day I may give a different answer, but this guy is always top 5.
Darkseid
Onslaught
DCAU Brainiac
Tony Stark
Hank Pym: You're taking over? Come on, give me one good reason why—
Iron Man: Three words. You're. Hank. Pym.
I've always been drawn to Thanos, Dr. Doom, and Magneto as my top favourite bad guys.
In recent years I've begun to appreciate the villainy of Ultron (though I haven't gotten around to reading Age of Ultron), and Loki.
Scarlet Witch.
Wasp.
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There's only DOOM!!!
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Doom doesn't back down, not even against gods.
Because Doom is a Man and feels a Man should bow to no one.
I'll chime in with Ultron and Thanos. I like Doom and Magneto, but they have been 'humanized' so much in recent years it's nearly impossible to think of them as straight villains anymore.
Surprised no one has mentioned Kingpin. Annihilus and Overmind are good when done well, too.