Hey, It's That Voice!: Chris Latta voices both Cobra Commander and Starscream, and exactly the same way, other than Cobra Commander hissing after an "s" or sometimes a "c". Other than that, they are the ssssame. (This later led to a semi-cameo in the Transformers episode "Only Human", one of the most solid links between the two franchises.)
In an episode where COBRA hosted a black-market telethon, they were originally going to sing a parody of "We Are The World" entitled "We Want The World!", but for whateverreason this never came to be.
Before Hasbro switched production company to DiC, Sunbow Entertainment planned a third season of the animated series set after the events of the movie. The premise of the season would have many of the Cobra leaders splitting into different factions, with Tomax and Xamot leading a criminal organization called The Coil while keeping the snake-transformed Cobra Commander as their pet (who would have later regained his human form and reclaimed his leadership of Cobra).
A sequel to the episode "The Gamesmaster" was cut, resulting in the Gamesmaster becoming a one-shot villain despite swearing revenge during his escape.
The basic story premise of the 1980s GI Joe was originally an idea for a Marvel Comics sequel series for Nick Fury: Agent of S.H.I.E.L.D by Larry Hama called Fury Force where Fury would assemble an elite commando unit for S.H.I.E.L.D. Marvel wasn't interested in that version, but when Hasbro approached the company about the revived G.I. Joe, they decided that a modified version Hama's proposal would work for them.