The "Joker Problem" is, in its simplest terms, based around the old Batman villain, first introduced in 1940. In his original appearance, the Joker was a homicidal madman who used complicated toxins to murder people as part of a crime wave that only he really understood. In his original appearances, the Joker was slated for death, because back then Batman routinely killed people or allowed them to die, but the editors realized that if they went around killing off all the good villains they'd run out of them, and so the Joker was spared. He went on to become Batman's greatest adversary.
World of Warcraft has a Joker Problem, because we keep murdering our Jokers.
Oh, it's hard to blame us - how many times have people pointed out how ludicrous it is that Batman or someone else hasn't murdered the Joker at this point? Plus, they drops shiny goodies when we kill them, and there's nothing players in an MMO like more than trinkets and baubles. Tirion Fordring once held a death sport that was entirely based around bribing us into gladiatorial combat with goodies, and we totally went for it. Sometimes we'd run that thing four times a week. But the fact remains - we barely get a good villain rolling for an expansion before we storm his or her castle, keep, subterranean lair, floating sky palace, old temple... you get the picture, I'm sure... and do war upon said villain. At the end, a sparkly corpse is left at our feet, the day is temporarily saved, and then someone else ignores all the evidence to the contrary and starts the whole thing up again.
Not all of the dead Jokers in our track were Jokers, of course. Some were Riddlers, or Penguins, or even just barely Calendar Mans. But we've definitely left a few Jokers strewn among the pile of dead would-be world destroyers, conquerors, and assorted evil people. Lady Vashj, Illidan, Arthas, Deathwing, Ragnaros, Al'Akir, Kel'Thuzad, Malygos, we've taken out some important figures with a great deal of significance to the setting. The up side is that it demonstrates the stakes and gives a player a sense of accomplishment to finally take down an archnemesis. The downside is, they're gone.