Okay, you may be sorry you asked. Top three in everything I can think of offhand:

Joes:
1. Duke
2. Clutch
3. Flint

Cobra:
1. Slice
2. Baroness
3. Destro

Autobots:
1. Optimus Prime
2. Prowl
3. Jazz

Decepticons:
1. Shockwave
2. Scorponok
3. Swindle

Marvel Super Heroes:
1. Spider-Man
2. Moon Knight (I'm a fan from way back, not one of these johnny-come-latelies who got on board because of his new comic!)
3. Captain America & Cyclops (tie)

Marvel Super Villains:
1. Hobgoblin (the original)
2. Thanos
3. Mr. Sinister

DC Super Heroes:
1. Green Lantern (Hal Jordan)
2. Batman
3. Superman

DC Super Villains:
1. Ra's al Ghul
2. Two-Face
3. the Riddler
(yeah, very Batman-centric, but I don't know a lot about the DC universe)

Star Trek characters:
1. Captain Sisko (DS9)
2. Worf (TNG & DS9)
3. Chief O'Brien (TNG & DS9)

If I come up with anything else, I'll add it here.

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is on indefinite hiatus...