Grand Unifying Guesses/G.I. Joe

The soldiers from all of the following are G.I. Joes

 * Transformers (in some cases, including the original cartoon, these canonically share the same universe!)
 * Cloverfield
 * The A-Team was being considered for recruitment before the infamous crime they didn't commit.
 * The plastic army men for small scale assaults
 * Sargeant Hawk and the Bravo Company Commandos for the same reason and as liason for the plastic world.
 * Skipper, Kowalski, Rico and Private head the animal division
 * Perry the Platypus, thought OWCA takes up more of his time
 * Pinky the Chiuhaha
 * Joker
 * Hawkeye Pierce
 * Guile
 * Cammy
 * Reese until he was forced to quit
 * Abby
 * Charles Charles, Dwight Dixon Ned's father
 * Shaun of the Dead
 * R. Lee Ermey
 * Bill Dauterive
 * Leroy Jethro Gibbs
 * Colonel Hogan
 * The Black sheep squadron
 * GI Robot
 * Wolverine
 * Captain America
 * Ms. Marvel
 * Vasquez before she dies.
 * Snoopy
 * Lemony Snicket
 * The Soldier They didn't much care for his severed head obsession.
 * BLU to spite RED.
 * Bill
 * Major Jackson Briggs and Sonya Blade.
 * L
 * Gandalf the Grey he (or someone) would need to be there to deal with sorcerers.
 * Hit Girl
 * Marv, he did say he fought in a war once...
 * Frank West he's covered wars you know...he never said which one.
 * Morshu unlikely, yes...but if he's like the demoman (as he is sometimes) he'd fit right in.
 * Catherine Aura she's in it to help make sure Cobra doesn't find out about her Earth...unfortunately they did without her knowing...
 * Orlando but the magic heshe proved too Ax Crazy for them so he/she quit.
 * Frylock
 * The White Shadow
 * Riff
 * Sam
 * Duke Nukem
 * Inspecter Fox
 * Tintin
 * Faith Connors
 * Grabovski
 * Aldo Raine
 * Jules Winnfeld

The following villains are members of Cobra

 * General Plastro
 * Starscream though trying to overthrow Megatron and command the decepticons takes up a lot of his time.
 * Doctor Facilier
 * Dr. Ivo Robotnik. Alias: Eggman
 * Dr. Insano
 * M.Bison
 * Count Olaf
 * The Fearsome Five
 * Vicky
 * Sky Marshall Wade
 * The Octopus
 * The Red Skull was offered a position but he turned them down.
 * Jackal and Hyena
 * Calvin AKA Fumbles is infiltrating the main GI Joe team.
 * Pigmar Dengar
 * Albert Wesker
 * Major Henry West a.k.a. Destro.
 * DOOFINSHMIRTZ EVIL INCORPORATEEEEEEEEEEED!
 * RED to spite BLU.
 * Norman Osborn
 * Jafar
 * Calypso
 * Needles Kane
 * The rebooted Krista Sparks
 * Nemesis
 * Rabbit's Revenge they might like like a neo Nazi esque group...but Cobra chose to make it into their branch of the group and weaken the country for their coming.
 * Vyvyan he doesn't care about world domination, he just wants to blow shit up.
 * The Goon for protection from G.I. Joe, just in case the CIA is so desperate to take him out they send them in.
 * Bun-Bun...but Cobra Commander is scared to death of him and only hires him when he needs something REALLY important done.
 * The Black Organization
 * Eric Cartman
 * Dogbert
 * The Fraternity, the idea for killing all the superheroes on their earth was actually Cobra Commander's idea...and he plans to use them in what could be his most dangerous scheme yet.
 * The Joker
 * Andrew Ryan
 * I.M. Meen
 * Mad Stan, eventually anyways.
 * Hans Landa