One of the most brilliantly disguised f***ed up episodes of any cartoon I have seen was an episode of Tom & Jerry Tales whose *entire* theme/punchline was the Black Plague. I think the title was "The Itch."  Now, I'm sure this started out as a challenge/bet among the writers over who could sneak in an episode about such a depressing topic and still be funny.  A touring medieval rat heavy metal band whose big hit song is "The Itch" causes its fans to scratch/spasm et al. The song is to the tune of "Ring Around the Rosie" (which, if you don't know the origins of, look it up ) and they are accidentally spreading fleas; they just thought their fans were dancing.  This is all while Jerry is trying to warn village guard Tom about what's going on and getting abused for it by him and a massive rat roadie / bouncer.  

They could probably do a whole Cracked article about this, if they haven't already.  Anybody got any others?