Behind all of the bad things that happen to Heroes there's always a villain - a sort of anti-hero in the literal sense of the word. Movie villains are not just behind the scenes guys - although they are also responsible for much evil-doing behind the scenes. They rule their criminal empires by fear and violence: even an old villain is fully capable of making the climactic fight scene worth remembering, especially since they never, ever fight fair. Thus, all villains are combat capable - whether it's esoteric kung fu or just a genius for brawling (when was the last time you saw the chief bad guy meekly surrender to the heroes?)
Villains are also equipped for more cerebral pursuits, and they almost always have masses of henchmen and a villainous lieutenant or two. That's one thing that distinguishes them from run of the mill bad guys.
What really distinguishes them from run of the mill bad guys, though is their overarching ambitions. They want to rule the entire world (or at least big chunks of it), eliminate all opposition to their power, control people's every actions or make everyone use Windows™. In other words, they really work at their evilness. No trick is too low - hostage taking, friend-of-the-hero-murdering, mass poisoning of the citizens: it's all in a day's work for a real villain.
