There will be plenty of comic book characters on this list, and virtually all of them are likely to come from the Marvel House of Ideas. If that troubles you, make your own list. I'm of the opinion that comic books, done well, are literature, and I've been pretty much exclusively a Marvel devotee since I can remember. And of all their characters I enjoy, Victor von Doom is my favorite. Brilliant, flawed, ambitious, stubborn, charming, gallant, even noble. He is firmly convinced that his enlightened dominion would benefit the world, even the cosmos. His only rule? Doom rules. Not the original megalomaniac, but perhaps the best, and the one who clatters around in my head as I try to craft my own villains. Cadmus from Minotaur owes no small fraction to the shadow of Doom.
My biggest question is how not one but two movie productions could screw this up. Heck, a Dr. Doom origin story, exploring his gypsy roots, the loss of his mother to Hell, his rivalry with Reed Richards, all of this is ten times as compelling than another hamfisted attempt to make the Fantastic Four interesting. Give me a hundred million bucks and a year, and I'd make a Doom film for the ages. Ah, well. I'll have to be content with back issues, I guess.