ha! Dukat was my first thought, too!
He's an incredible 'villain' because he's such an excellent character. Everything he does, he does for a reason, and it's mostly for fairly unselfish reasons too - he's as much about Cardassia as he is about himself.
That said - my vote has gone to the Borg. I think they represent such a perfect villain to the Federation because they are so similar, yet so different. The Borg want to unify everyone as one peaceful whole, not that dissimilar to the Federation. But obviously their methods differ... and they are in many ways the antithesis of the Federation - diplomacy simply doesn't work on them. They can't be bargained with, or talked around with a well-reasoned Picard monologue.