Crow: This is why the dinosaurs died out. You bored them to death!
Running Gag: Joel and the 'bots keep singing the Bunny Hop as the cavemen go hopping through the jungle.
Shout-Out: Several references to F Troop, since Frank de Kova (who played the Black-Bearded One) was also in that show.
Take That: Roger Corman's quick-and-cheap filmmaking methods are the target of several quips, including a suggestion that Robert Vaughan not eat the squirrel he's cooking so Corman can use it as the monster in his next film.
The MST3K treatment of Aquatic Wizards provides examples of:
Joel: Miles from the dock and they can't swim, I love that trick!
Gender Is No Object: Water-skiing is shown to be enjoyed by both genders, albeit slightly segregated for instruction.
Male Gaze: Par for the course, considering the ubiquitous swim-clad women, with the narrator admonishing the viewer for (presumably) ogling the bare legs of multiple women presenting different types of water-skis.
Mr. Fanservice: The camera takes a few lingering shots of the rather well-toned physiques of Alfredo Mendoza and "Chad Slabbody".
Narrator: Well, this is a different assignment, and a true depiction of actually filling an order [Ross] recently received.
Joel: Kill Colonel Kurtz!
To A Night at the Opera: After the narrator lists the animals in Ross's order (one bobcat, two bearcubs, and three rattlesnakes), Joel adds "And two hard-boiled eggs! Make that three hard-boiled eggs!"
Narrator: Here's the shed. (in reference to a snake's shed skin)
Crow: Two Sheds?
Take That: This short is followed with a host segment entitled "Catching Ross", wherein Joel brutally torments an action figure modeled after Ross while Tom mocks it. Fans complained when the short was put on a collection without "Catching Ross" included.
The bots are also eager to whip the piss out of the narrator of the "Aquatic Wizards" short when he refers to a Hispanic waterskier as a "Mexican jumping bean."
Crow: "This time, the white fascist narrator will make a racial slur!"
Tom: "Hah, but what do I know? I'm only a fat hick announcer, mowing down pretzels and pinwheel cookies, and trying to come to grips with the tattered ends of a once promising life gone horribly wrong, God, God, why, why?!"