Had to go with Annorax, oddly enough. VOY had its problems but he was one of the best Trek villains period, chillingly monstrous with a psychologically realistic core, and more truly heinous in the larger sense than Khan.
My first pick would have been Kivas Fajo -- am I going to cause angst by asking "why no Kivas Fajo"? His is a much more personal, intimate heinousness and in some ways more creepy and effective because of that; he's no world-destroying super-baddie, just a greedy, petty, pretentious sociopath, and he's all the more memorable for that.
I agree with you--in old Trek I'm reminded of Parmen in this mold, and he was a lying sadist, but Fajo certainly had more style. His general cheerfulness was super-creepy.
I'm going to put in my own vote for Weyoun for second place: smarmy, machinating, and coldly but affably uncaring about anyone or anything else but himself and the Founders.
And 3rd...the Vidians as a species. Not evil, per se, just...heinous. I mean, we're talking Frankenstein stuff here. With live