I find villain games are best when the party has a goal... not "muhahaha evil" but "the forces of good simply don't understand my genius" sort of goal. And it must be either one goal or a set of closely related goals. For example, I had a character that was a necrocommunist... he wanted to kill the powerful undeserving lords of society and use their undead remains to farm fields and do other grunt work, so that the more deserving folks (laborers, farmers, etc) could relax. And anyone not like him? They made good corpses too. Also he wanted to be adored by his people, so those spreading discontent must be enemy spies. They should be killed too, and raised as more undead to handle more labor...
And another guy in this party was a Paladin of Tyranny who just wanted everyone to recognize one leader, because that's how society functions best. So he picked my Necromancer as that one leader, and slaughtered anyone who opposed him, while being fanatically loyal. These two characters made a great team. Characters like that could be great for a villain party. Might also throw in a mad scientist who just wants recognition of his genius (Artificer perhaps?) and an assassin bent on purifying the world of chaos and you'd have an awesome team of crazed zealots who were sure they were the good guys.
Run a campaign like that, let the players loose on the world and let them remake it in their insane, twisted image. Then start a new campaign, a few hundred years in the future, where the old PCs are still in power (with various life expanding techniques, of course), and this new team of level 1 upstarts are the real heroes who must overthrow the villains... now the last campaign was just building the campaign world for the next one!
JaronK