Good grief. Whose stupid idea was that?
Actually, mad props to the Jack Bauer contribution.
Thought of another one: Tommy Gavin, Fireman. Codename…uhhh…Smokejump?
“Blowtorch”. 
Earl Basset, expert on monsters. Codename: Graboid
Hrm…continuing the WWF/E theme of Sarge and Piper…
For Joe:
The Rock - Communications. Secondary Speciality: Cook.
For Cobra:
Vince McMahon, Codename: Chairman - Propaganda and recruiting.
There’s already a Joe named Blowtorch. The other flamethrowers of the team are Charbroil, Blast-Off and Ice Cream Soldier. The firefighter is Barbecue. That’s why I settled on Smokejumper, but that’s really not what Tommy does…
Dear God am I over thinking this or what?
The NCIS or JAG guys would definitely be on the team as support members, with “Bugsy” and “Eyes” (Good call - but I’d go with Shawn Spenser, Codename “Psyche”!)
There’s also one named “Maverick”. 
Every team needs an off-kilter member: Why not Darkman? Codename: “Nobody”.
Just as an aside, I would wager that, for many children of the 1980s, this was where we first learned of the Warsaw Pact.
Major Alan Schaefer “Dutch” - Skills: Team leader Special Forces, Infiltration and extraction. Other skills: Extra-terrestrial extermination.
Cobra villian:
PeeWee “Crank one out” Herman.
Primary attribute: Enhanced wrist action.
Skills: Starts screaming and flailing about when Joe says special code word resulting in annoyance to Joe and depletion of his ammo supply.
Minor skill: Some ability to lurk in dark theaters.
Liabilities: Likely pedophile.
Drats, I was going to suggest these.
I know Aldrin got a 12" figure but I don’t know if there were any plans on putting him into the smaller line.
Doc Holliday - Code name "Huckleberry"
Can outduel anyone in a gunfight- while smoking a cigarette, yet.
[hijack] I’ve been reading those file cards. Isn’t it a little cruel to codename a guy “Hit’n Run” whose parents were killed by a drunk driver? Still, those cards are VERY fun to read.[/hijack]
The ‘Rocky’ one I suggested was… planned, but never completed. He did show up in the comic book. And his opponent was made: Big Boa.
If we’re doing WWF/E guys you’ve gotta have Mick Foley in there. He’s not the toughest of the tough guys, but his reputation for psychotic acts of violence causes Cobra to have an almost supernatural fear of him and leads to the following dialog among the Joes.
“What is his deal?”
“I don’t know, I’m just glad he’s on our side.”
“Is he, really?”
“So far.”
Also, he has three nicknames.
Dr. Gregory House, codename “Cranky”.
Not the most liked of the team, but very useful whenever Cobra decides to spread mystery illnesses to threaten the world.
Catchphrase “It’s never lupus”.
It’s kind of sucky how they made the leader of the entire MASK unit an E4? WHy’s he a Specialist?
Maybe it’s branch specific [del]army[/del]joespeak, and he’s actually a civilian contractor. 
Okay, at the risk of being over creepy/geeky, howsabout:
Kim Possible! Code Name—probably just her name, minus the space and the uppercase “P.”
“She can do anything,™” or so goes her tagline. With the added bonus that she already has a ready made battle uniform; it just needs a bandolier with some extra weapons and grenades that she never actually uses.