Actor Allusion: In one scene of "Murphy Murph and the Feng Shei Bunch", Marco wears a Chips helmet.
Executive Meddling: The episode "Feast of Alvis" was supposed to be a straight-up Christmas Episode... until the executives rejected it. Jesus was then replaced with Alvis, the worship of whom served to make Murphy look that much crazier.
Sparks: Your "lord"? It's a baby with a freaking gun, roasting over a flood light!
Promoted Fanboy: mcheshpants420, a member of the [adult swim] message board, who wound up writing "Fusebox" and "Dearly Beloved Seed". It's generally theorized that this is mc chris, one of the writers on the show and the voice of Hesh, simply mocking the fans.
Throw It In: Aside from the Hilarious Outtakes that sometimes play over the end credits, several lines throughout the series appear to be lines from the recording studio where the actor was talking to the director or otherwise cracking up. Debbie Love seems to get quite a few of these, and one particularly odd one involves Stormy, sounding unusually eloquent, arguing about whether the line should be "sticking a staple in their eye" rather than "sticking a stapler in their eye", finishing with "maybe I'm being too literal, I mean, this is a cartoon."