My choice was Darth Sideous, a.k.a. "THE EMPEROR"
TBH, I never really thought that Darth Vader was a true villain. I mean, even before Episode III, me and my dad always thought that Vader was a good guy who just got mixed up with the wrong crowd, didn't even really consider himself to be evil; like in Episode III, he honestly thought he was doing the right thing. Darth Sideous KNEW that what he was doing was wrong, and did it anyway. To me, the raw evil passion that Sideous had puts him miles ahead of the other villains, and it is what makes him my choice. Agent Smith was a machine, and I think that, in the first Matrix, he explained himself and his beliefs very well, and I actually found his "humans are a disease" speech to be very logical, it made sense. Khan was a great villain, but what made him likable was not his pure evil mindset (which he did not have) but rather his rage, his thirst for vengeance, and his intellectual manner. Khan was like Moriarty, Darth Vader was like Marcus Junius Brutus, Agent Smith was like HAL, but Darth Sideous was like Satan. NOW you probably understand my decision.
"To boldly go where no man has gone before"
--ADMIRAL JONATHAN ARCHER--