In terms of characters, my Joeverse is more or less in line with the comics just in a modern day setting. The settings tend to be a little more grim though. I grew up reading hard-boiled crime novels, and my Joeverse just sort of reflects that.

My Sigma6 verse is pretty different though:

!. The old joe team was disbanded in favor of a smaller unit more focused on espionage and counter-intelligence than large scale warfare

2. Cobra Commander is dead, and Cobra in general is on the verge of extinction.

3. Long Range is not officially a member of the joe team. He quit after pulling an op that left him kind of messed up in the head. He is a freelance operative who still works with the Joes on occasion, and a borderline alcoholic.

4. Many members of the Sigma 6 team don't fully trust Duke. His extensive experience in covert and black ops has made him a man of secrets. He knows where the bodies are buried, because he put a lot of them there.

5. Lt Stone is dukes 2nd in command, and a confidant of sorts. Stone was originally the "handler" for the Renegades. He acted as a liason between them and the Joe team proper.

6. Destro's son, Alexander exists in my Sigmaverse.