For me, the best villains remain: Khan and Soran. Special mention to ST: TMP, simply because it's idea of an antagonist seems to be more in line with the original series.
For all the talk of his brilliance, Khan was an elitist driven by anger and revenge and it certainly clouded his better judgement. And the best part is he wasn't a new villain shoved in, he was already established with an episode.
One of the things not touched on to a great extent, are the consequences of actions in the Trek universe, and the Borg creating a villain out of a person who might have simply gone to to lead a life of scientific study and research on his home world, created an unlikely adversary; an adversary not driven by revenge, power, wealth, simply the want to be in a happier place where he might join his family again. Unfortunately this strong desire yeilded truly evil actions.
TSfS had a midiocre Klingon adversary seemingly just to fill a void.
TVH[/i] had no villain, instead opting for a phallic-shapred probe with one ball that decided to tear apart the home environment of the one species of whale it can't find (fuck all the other whales, right).
TFF just featued a delusional man who went too far to see his goal achieved. Not necessarily a villain.
TUC is a second palce runner up for the best villains placing.
ST: FCwas crap. It ruined the Borg almost as much as Voyager did, and gave us a lead villain who seems to be rather inept for such a superior power.
Insurrection -- please, this was a joke. Likewise Nemesis. To think back that these are how the TNG movies ended, makes you just want to balfe all over the place. No proper send off, just a giant galactic middle finger.