Mike: "Come on, beer, get in my mouth. Come on!" Crow: "You know, after this beer, we should have a beer sometime." Servo:(as the Devil Fish) "I'm a recovering alcoholic. I can't eat that guy."
Brief Accent Imitation: At one point, Bob says "I knoooow!" (which was also used as the stinger). But he says it differently than the rest of his lines in the movie. Tom observes: "Was this guy dubbed by J. Peterman?"
Censor Box: The MST3K logo was used to cover up a surprise guest appearance by Peter's balls. "Dah! Incoming!"
Servo:(as Peter, giggling) I hung one out for fun!
Everybody Laughs Ending: The movie ends with a small joke. Crow and Servo decide to laugh for the duration of the end credits in response.
Foregone Conclusion: Servo says "If I don't come back, adopt a single currency, eat snails, and don't shave your armpits" when Peter goes into the water for the last time. Peter survives unscathed, but evidently Europe decides his suggestions are worth implementing anyway.
Genius Bonus: Mike has a fairly elaborate Running Gag involving outboard motors. Whenever one appears he makes suggestive-sounding comments about them ("Hey, nice Evinrude." "I hate when I get my Evinrude tangled up." etc). Evinrude is, of course, a brand of outboard motor. So is Johnson, which is clearly what Mike means to say whenever he says Evinrude.
Gonk: Mike and the Bots repeatedly joke at how ugly Miller the Killer is, with Crow even speculating his sheer ugliness fuels his boat.
Incredibly Lame Pun: Servo jokes about the Devilfish having "eleventacles." Mike groans audibly. He also groans at Servo's "We're experiencing tentacle difficulties!".
Ditto for electricians, though largely because they have an alliance with the dolphins.
The Red Stapler: The electrician that comes to the SOL mentions that guys like him have been getting a hard time from people ever since this movie came out, forcing them to make an alliance with the dolphins for protection.
Refuge in Audacity: Pearl turns up the "Italian Stereotype" vision mode on Mike and the Bots until they become full-on pizza spinning, loafer wearing, gondola riding ethnic slurs.