I like Ganodorf in OoT, apart from the obvious, because he's cunning enough to get the King's favour and cheat even the most distinguished people in the realm (I'm assuming here that Hyrule's Castle is not full of idiots who cannot spot a maniacally laugh at sight). He's total boss and the ever King of Villains.
However, my favourite villain is Skull Kid in MM. I know the true villain is the mask itself, but Skull Kid is the one doing all the evilness: he had some sparks of evil within him, and Majora mask gave him power to expand this evil inside him. So what he does, he does it because he wants and the mask enables him to do it. I like him the most because he's very imaginative and his tricks go from mildly annoying jokes to heartless cruelties. And with the mask on, he's cute ;P