Brick Joke: During the third host segment, after Mike keeps falling asleep at the wheel while driving the SOL, Tom demands to take the wheel, insisting he's an excellent driver. At the start of the next segment, when Mike and Crow walk in on Tom behind the wheel?
Butterfly of Doom: The narration at the start of the film attempts to invoke this trope after Stock Footage of a volcano erupting is used to explain the Mantis' awakening. This does not go un-riffed:
Narrator: For every action... Mike: ... there is a Jackson. Narrator: ...there is an equal, and opposite, reaction. Mike: (as the map on-screen pans north) We take you now to a coldwater flat in Brooklyn, where another volcano is erupting. Servo: (when map pans to the North Pole) Because of volcanic activity, a creature named Santa Claus crawled out of the ice!
Deep South: The radio stations the crew pick up makes Servo wonder if they're in the Southern portion of the Milky Way.
Dirty Coward: One of the tribesmen abandoning another when the mantis attacks:
Servo: Good luck!
Dress Code: In the opening host segment, Servo announces it's "Business Casual Day" on the SOL and berates Mike for his alleged violations of the (non-existent) dress code.
"Let's review: No chaps without pants... Mike. Number two: No sheer camisoles... Mike. Number three: No toeless shoes or sandals or spike heels... Mike."
General Failure: "Sir, I just remembered you didn't tell us what your plan is or anything!"
I Am A Humanitarian: During a host segment, the SOL runs into a space creature. Bringing it aboard, it takes a liking to Crow and tries to eat him. In the last host segment, Crow reveals that he cooked it and served it as a meal in response.
Interspecies Romance: At the end of the episode, Mike and the Bots receive a letter from Peanut (Bobo's assistant). It's revealed he survived Earth's destruction - getting blasted into 2112 Wisconsin and meeting "a nice girl" - a Nelson woman.
Crow: It's certainly a joyous day for any Nelson woman when she meets the ape of her dreams.note Servo: I'm hiding my sock monkey, that's for sure.
Mike Nelson, Destroyer of Worlds: Mike's reign of terror begins when he inadvertently helps Prof. Bobo and Dr. Peanut detonate a thermonuclear bomb. While Mike later tries to protest that they'd have blown themselves up anyway, odds are that Pearl would have seen what Bobo and Peanut were doing and stopped them, if not for Mike happening to throw in a suggestion on how to activate the bomb.
Skewed Priorities: Crow's main concern about Bobo and Peanut helping the religious cult detonate the "holy and everlasting Bomb" is that they're doing that instead of providing the Satellite of Love with this week's movie.
Stable Time Loop: Peanut is sent back in time by the bomb's explosion, where he marries into Mike's family, helping to cause the eventual Ape uprising... which eventually leads to Peanut's own birth and being sent back in time. Yeah, this is one of those occasions where the MST3K Mantra helps.