[Guiron chops one of Gaos' arm-wings off.] Crow: All he's got is a wing and a prayer. He's really going out on a limb! He's winging it!
In the Style of...: Michael Feinstein (played by Michael J. Nelson) treats us to a Cole Porter-esque piano version of Gamera's theme music at the end.
Insistent Terminology: Tom gets more and more frustrated that they keep calling the planet that they're standing on a star.
As mentioned on the movie recap page, this was because Sandy Frank couldn't be bothered to copyedit the script, which was a direct and slavish translation from the Japnese. In Japanese, "star" and "planet" are the same word.
Lampshade The Obscure Reference: At one point, Tom says "Stop her, she stole Mike's keyboard!" Crow is puzzled, and Tom admits it's an obscure reference. (as explained in the Amazing Colossal Episode Guide, this is referring to staff writer and future host Mike Nelson's girlfriend breaking up with him and stealing his keyboard)
Memetic Mutation: invoked Gamera's gymnastics became a part of MST3K's opening credits.
Mondegreen: Joel and the 'bots insist on calling Kon-chan "Cornjob".
Oh Crap!: When Gamera jams a missile into Guiron's head and sets it on fire.
[Closeup of Guiron's face] Crow: Oh, damn. [EXPLOSION]
Celebrity Resemblance: It's repeatedly noted that Tom from the film resembles a young Richard Burton. Gamera's resemblance to Karl Malden (especially his nose) is a Running Gag throughout all the Gamera episodes.
"Hello! Thank you!" Joel and the 'Bots hit the ground running with that infamous scene. (Thank you!), and the jokes continue all the way through to the Gamera Vs Zigra episode. (Hello!) Bonus points for the riff of the end of the scene, when Tomoko appears in the back seat while Tom's mother is driving away.