Kahn, because he's one of the most suave space villans ever.

Megatron! He was unusual amongst 80s cartoon villains, in that he wasn't insane and had goals in mind (though they changed in scope often). It was more than just "He's evil. Duh."

The Ori from SG-1. It took 11 years, but they finally wrote a villain that's nigh unbeatable. Though I hove no doubt that they eventually do defeat them, even if Jack isn't on the team anymore.