1) Prominent role played by Polly.
2) Snake Eyes breakdances.
3) Heavy Duty says, for no apparent reason, "Mister Body Massage machine, go! Body massage!"
4) Opening is a shot-by-shot live action remake of the "Battle for the Statue of Liberty" opening to the original GIJoe: The Movie.
5) Cows. Lots of them. Being thrown into buildings. (Hey, it was the only saving grace in Stephen Sommers' last piece of crap movie, Van Helsing.)
6) Two words: Sergeant Slaughter!
7) Footage of Yul Brenner from various old movies digitally spliced onto a bodybuilder's body to appear as Doctor Mindbender.
8) Duke killed in action. Scarlett and Hawk cry loudly, and are poorly overdubbed saying that he'll be okay. Another poor overdub, of Doc, over the final scene, saying that Duke has come out of his coma.
9) Tomax and Xamot played by Cheech and Chong. Cue the Corsican Brothers references!
10) Renegade SAW Viper misinterprets an order from Cobra Commander and kills the entire Joe team, as well as the film crew.
11) Bill Ratner appears as Flint in a post-credits PSA, warning kids not to hide in abandoned refrigerators.
Feel free to add more.