It's worth noting that the Big Bad goes by 'the Doctor' before being outed as Cobra Commander.
Storm Shadow puts his swords together into a double-sided staff thing when fighting Snake Eyes at the end. Snake Eyes is played by Ray Park, who did Darth Maul, who was armed with a double-sided lightsabre staff.
The director brought a buttload of Mummy alumni with him. Besides Arnold "Imhotep" Vosloo as Zartan and an uncredited cameo by Brendan Fraser as Sgt. Stone, there's a very short scene with lovable traitor Beni (Kevin J. O'Connor, who Sommers casts in every movie he's made since Deep Rising) as evil scientist Dr. Mindbender.
Cobra Commander was given a new look because of the fact that Sommers thought that giving him a hood (or even a ski mask) would make viewers think KKK member when they saw him. Nor would they justify a form-fitting, featureless steel face-mask, since they wanted Joseph Gordon-Levitt's face to be at least partly visible.
Similarly, GI Joe becoming an international task force was done due to Paramount/Sommer wanting a high overseas box office pull for the film and thinking an all-US team of soldiers would not sell tickets outside North America.
Though, both of these plot elements (Cobra Commander's face-mask and GI Joe being an American military team) are brought back for the sequel.
Race Lift: Ripcord is white in the original series. Breaker was a white southerner in the original Marvel comic run. Heavy Duty was still black but from Chicago, not London.
Stan Winston: The effects team behind the accelerator suits.
Throw It In: Ripcord's helmet flashing holographic pictures of Scarlett. Originally, he was meant to be responding to the amount a virtual controls showing up in the HUD, but when it got to actually including the display in the visual effects department, they thought it'd be more amusing if it had her face popping up.
What Could Have Been: Rapper Common was offered the role of Heavy Duty's cousin Roadblock, but film screenwriter, Stuart Beattie, chose Heavy Duty instead.