I think Kai Winn is the best of the recurring TV villains. I HATED THAT WOMAN. Followed by Seska and Maj Kullah(sp?), who were more like recurring annoyances for the Voyager crew. I did not like the Duras sisters of TNG one bit. LAME. Gul Dukat was okay, but overstayed his welcome by about a dozen episodes. The Borg Queen was good, but became far too petty for what she was supposed to be. The female Changeling was a nonentity. The Xindi weren't truly villains. Future Guy was a plot device. Sellek was good, but also not a true villain.
In the movies, Khan was decent, but is often overrated. Kruge was a good if bland baddie. Sybok was a good character, but not a villain. Soran could have been so much better. I actually liked Shinzon, the messed up Picard-that-could-have-been who despite all he endured, still managed to achieve ao much. I liked Nero too, he was an angry space trucker who I pitied more than anything.