The MST3K presentation of this movie contains examples of:
Accidental Misnaming: Joel and the Bots mishear Bix Dugan's name as "Big Stupid", and keep referring to him as such.
Alternate Ending/Fix Fic: The final host segment consists of Joel and the Bots rewriting the ending to remove Carrie's death from the plot. The Amazing Colossal Episode Guide explains that this really was very therapeutic for everyone involved with the show.
Contemplate Our Navels: Literally — Crow and Tom each drill themselves a bellybutton. Upon getting his, Crow starts contemplating it.
Canon Discontinuity: Crow and Servo, upset at the ending, come up with their own instead, which involves Carrie living, Jack Elam getting abducted by aliens, Danny and Bix taming dinosaurs in a post-apocalyptic world, and a kingdom of pygmies. Caught up in the general enthusiasm, TV's Frank comes up with his own, which involves Bix as a being of pure energy.
Ho Yay: invoked "And once again, Bix saves Danny from a heterosexual experience."
Joel: (singing) The Girl In Lovers' Lane... Crow: With Jack Elam, not Jack La-Lanne. (Servo: Not La-La-a-ane...) Joel: And lots of actors, there's no time to name... Crow: A screenplay by Joe Heims that's pretty lame. (Servo: Pretty lame...) Servo: The entire crew, feels a sense of shame. (Crow: Shame.) If only they'd had / half a brain / they could attain / a measure of fame / from a film like Shane! / But no. To their disdain, / The Girl In Lov-ers Lane! Joel: (Makes Rawhide whip crack noise.)