I never put a lot of thought into the full scope of my world, but it more or less follows the comic book continuity. All the major events of the Marvel run happened in one form or another, except for the killing off of several characters. But I tend to use the cartoon characterizations more than the comic book ones (except for characters who were barely in the cartoon, like Stalker). I disregard everything that happened after Marvel (Devil's Due, I'm looking at you!).

As you can tell from reading the TF crossover, my main Joe team consists primarily of the members who were featured in the cartoon (1982-1986), with the latter-year characters serving as reservists and expanded team-members who are called in to augment the existing team. The new characters from the JvC/Spytroops/VvV years are new recruits to the team. I actually wrote up a chain of command for my Joe team some time ago. I think I know where it is, and if I can find it, perhaps I'll post it here.

Cobra in my world is run by the triumvirate of Cobra Commander, Destro, and the Baroness. Major Bludd, Scrap-Iron, Firefly, Tomax and Xamot, and Dr. Mindbender are the second tier of the main Cobra leadership, with other named Cobras augmenting them but holding no real place in the chain of command (Slice and Dice, Scalpel, Interrogator, Croc-Master, etc.). Serpentor happened, as did Fred VII, though maybe not exactly like in the comics. Cobra Island is their base, though they have strongholds all over the world. The Cobra Consulate Building in New York City also exists, and Tomax and Xamot pretty much run it.

Action Force is in my Joe world, and much like msu44 said, it includes members like Big Ben and Action Man. The leader is Lt. Stone, based upon the Sigma Six character. I don't have them very fleshed out, and I don't even have figures of some of them, but I'd get/make them if the need ever arose. Action Force's main enemies are the Red Shadows, though I don't own any of those either. Action Force is mainly there to be spoken of and not actually seen in my world.

SKAR (of G.I. Joe Extreme) probably also exists, though again, they'd probably just be mentioned and never actually seen.

Finally, though my stories pretty much take place in the modern-day real world, there is one big difference-- In this universe, the Soviet Union still exists, and therefore the Oktober Guard are around and just as formidable as they ever were.

Oh, and in case you couldn't tell, the Transformers are there too! As I've said ad nauseum-- If the Punisher and Galactus can exist in the same world, and if Batman and Superman can exist in the same world, there's no reason why G.I. Joe and the Transformers can't exist in the same world!

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is on indefinite hiatus...