So, anyone who’s played D&D more than once knows that the PCs will kill the villain as soon as they get the chance. True to murder-hobo form, they’ll even execute the guy if he surrenders, or is knocked unconscious (or is otherwise helpless). After all, you know if you don’t kill the BBEG, he’ll just be back, bigger and badder than ever…loose ends and all (which makes the PCs sound rather villainous, doesn’t it?).
Of course, the players kill off the BBEG ASAP because, well, they’ve no reason not to. They get the XP for defeating the villain (and his minions), as well as his loots, so why not tie up those loose ends?
But what if we give the players an incentive to not do the smart and logical thing? If they players let the BBEG live, they get double XP for defeating him/her (or triple, quadruple…whatever it takes to make it worthwhile). This only applies to major villains, and perhaps favored lieutenants, but not to the lackeys.
How exactly the villain “lives” can be left up to the GM and the players: maybe the villain is imprisoned (and later escapes, natch), or a PC hesitates and the villain is able to make a hasty escape…whatever sounds cool, or works for the story.
So, the GM gets to keep a cool nemesis around for at least one more appearance, and the PCs have a reason to do the “right thing” (other than just being a bunch of chumps who let the bad guy get away).