Cool list!

I basically divide mine up into environment/missions - without consulting my list or actuall figures, here's what I remember off the top of my head (I'm only listing the Joes that I actually own, so for instance if you don't see Joseph Colton on my list anywhere, it's because I don't have his action figure yet, not because I don't recognize him as an important part of my Joe-verse):

Headquarters/Continental U.S. Missions:
Led by Hawk, with Stalker second in command.
Snake Eyes and Grunt usually buddy up (when SE isn't with Scarlett).
The rest of the O-13 join them with the MOBAT, RAM, VAMP, and APC.

Desert Operations (Either the Utah PIT and/or the Middle East)
Duke leads team with Dusty as his eyes and ears.
Basically all of the desert-colored Joes you'd expect (Repeater, Skidmark, Spearhead, and Tan Clutch, along with Recondo, as he always looked more desert than Jungle to me.

Jungle/Forest Warfare Team (I do like to differentiate between the two)
Beach Head with Falcon as his apprentice lead Leatherneck, Ripcord, etc.

Swamp/Bayou
Gung-Ho & Muskrat

Urban Strike Team
Shockwave heads this unit with Hit & Run, Low-Light, Airborne, and 1986 Roadblock.

Snow Force
Snow Job, Frostbite, Iceberg in the Battle Bear, Blizzard, QK, Bazooka, Alpine.

Rescue Squad
Airtight, Barbecue, Tripwire, Doc, Lifeline, & Blowtorch.

European Missions
Flint, Jaye, Crankcase, Big Ben

Sea
Shipwreck, Deep Six, Cutter, Torpedo, Wet-Suit

Air
Wild Bill, Crazy legs

Serenghetti/outback/plains
Outback, Ambush

They can cross-over of course, but these are usually the names that come up, for the specific areas of the earth.