Recently PC Gamer posed a "Best Villain" question similar to last week's at Gamespot. Jordan Crafts' letter was published in a recent issue of the magazine. You can find their "Best Villian" letters here
Colonel Blair’s Archenemy
Okay, I know this is gonna sound old, but the best PC game villain has to be Prince Thrakhath from Wing Commanders 2 and 3. I guess it would help to have read the novels to know what a devious scoundrel he was, but he easily gets my vote as top villain.