Since I'm always curious about the references of some of the more obscure jokes, I thought I'd start off with a few I know.
"This goes out to a guy I like to call 'Dad'"--Shari Bellefonte-Harper, the speaker of this line, is the daughter of Harry Bellafonte, actor and calypso singer. He sang "The Banana Boat Song", featured memorably in "Beetlejuice."

Doctor: "Are you saying that this fungus..."
J & Bots: "...is a mungus!!"

For some reason, when the credits show, I always laugh when Joel sings "This movie sucked!!"

He was quite right. I think pretty soon, archaeologists will dig up Ben Murphy's career.

The scene where the mummy is gliding outside in the moonlight and Joel says, "He's at the airport!" Always cracks me up.

This movie is really awful. How can you forget when the Tony Robbins look-alike guy gets the fungus all over his hand? AHHHHHHHHHHHH!!!!