I still haven't voted yet; I can't decide which of the following to vote for:
Stromboli: That the man has only two scenes and a relatively minor role, but has still left such a lasting impression after all these years really says something. He's the only male villain who succeeds in being both funny and scary.
Chernabog: Need anything be said? I love the Kay Nielsen design and the Bill Tytla animation.
Captain Hook: I'm very tempted to go with Hook here. A more complex caracter than really meets the eye. When I was young, I
always went to fancy dress parties as Hook and pitied those who dressed up as Peter (who is still one of Disney's best heroes)!
Shere Khan: I simply cannot believe that Scar is winning with Shere Khan receiving no votes at all. He is practically the embodiment of the suave, sinister British baddie. Scar
wishes he could be like Shere Khan.

Without a oubt he can be described as the 'coolest' character Disney has created. His upper-class approach to things is really what makes it one of my favourites. Shere Khan really couldn't be bothered with "all that" and was so awfully polite.
Prince John: Quite simply, great animation, and the funniest character Disney has created, in my opinion. Peter Ustinov's voice is brilliant, and his chemistry with Hiss is brilliant.
Professor Ratigan: A Disney Villain voiced by Vincent Price is a dream come true. A complex character; he resents his common, savage nature and hides it with a facade of respectability. Probably my favourite Glen Keane character.
Judge Claude Frollo: Another complex character, and a very applicable allegory to today's authority figures. Frollo is a worthy successor to Cinderella's Lady Tremaine, and his little side smirks and prudish sneers add to his character. Hellfire is his best moment. An excellently developed charagter.
Hades: A brilliant design from the great Gerald Scarfe, and beautiful animation. Once again, Hades is torn etween two sides of his personality. This is one of those cases when the minions bring out the best in the villain. James Woods' voice seems to have been the catalyst in defining this character.
Granted, I have listed more than half, but it is a difficult decision!