Although arguably the chicken-duck is pretty funny, I think Minecraft should have it's share of running gags built into the game. Some subtle, some a bit less so. Here are a few suggestions, though I am open to others.
Staring at a window (not block of glass) for a long enough period, you have a very slight chance that the face of
Herobrine a creeper will appear for just a few seconds.
Once in a very very rare while something other than a chicken will hatch from an egg.
One in 50 chance of a villager being "insane" (offering the most ridiculous trades imaginable). Insane villagers would also have some bizarre behaviors, though what specifically I have not figured out. Also a chance that one of these villagers will rip you off (OF SOMETHING NONVALUABLE) give you nothing in return for payment, and go "Haha!" and run away.
On rare occasion you may see hearts rising from a villager and an iron golem. Things that make you go "Hmm!" <villager voice>
... This is one suggestion: "Add humor to Minecraft", not a wishlist. The thread is about how.