Varies, depending on the campaign. However, this is the most common of the themes that my players have seen...
1. There is a clearly Evil uber-villain (generally Epic-level) that is "behind it all". The uber-villain is generally identified fairly early in the campaign, and is clearly out of reach for the PCs. Maybe it's Orcus, or Kyuss, or something similar. The uber-villain is too far above the PCs to mess with them until the late stages of the campaign, and then he's fairly straight-forward in his evil - laying waste to cities, bringing about the downfall of emperors, and seeking to crush any opposition in his way. If he encounters the PCs, it's a fight-to-the-finish... unless he or they somehow escape the battle. Then it becomes a matter of cold revenge, and all bets are off. I've seen atrocities on both sides in these kind of protracted duels: lawful good PCs sacrificing a soul-trapped NPC to Lolth in the Abyss to ensure he stays dead, chaotic evil villains killing/skinning/wearing a PC's beloved father to provoke him into a final confrontation, and worse.
2. There are one or more shades-of-grey NPCs. These are the guys who really fascinate my players. They might be a patron, or a temporary ally, or simply a contact. My players have learned that the really nasty stuff generally comes from the NPCs, even though they're also gaining significant benefits from them (e.g. a devil's deal). My shades-of-grey NPCs usually stick to psychological and alignment damage: they don't kill, abduct, torture or steal. Instead, they trick, bribe or convince the PCs into doing the killing, abducting, torturing and stealing. My players hate these guys more than the "true" (?) villains, even though they also can't entirely do without them.
3. ...and finally, there are the single-module or short-arc villains. These are generally servants of the uber-evil from category #1 above. Their actions depend entirely on their motivations. The worst I've ever inflicted on my players was a ghastly affair where a pacifist combat medic (long-running henchman) was separated from her primary PC for a time, murdered by a supposedly-friendly gnome NPC, who then hollowed her out like a gourd and stitched himself up inside the corpse. He used magic to masquerade as the medic for several sessions, only revealing himself to the (horrified) PC at the worst possible time by cutting his way out while the PC was asking for aid in a crucial battle.