I've faced this question myself -- as some of you know, I've been taking a series of "class reunion" shots; group pics with all the Joes who joined the team (ie character first had a figure released) in a particular year. I'll probably post them at JoeDios when I have every year done, but there are characters I don't have any figures of yet (Starduster, Hardtop, Cold Front, etc...).
I was presented with the choice of which version to use from my collection; I was influenced by the comics since I follow them so closely, and being reunions it's how they could look now as opposed to back in the day. You can see the ones I've done already
HERE .
So with that in mind, here's my list for this thread:
1. Duke - VvV (o-ring, not buttplug)
2. Roadblock - Spy Troops
3. Beachhead - VvV (I do like the JvC design but the proportions are too much)
4. Scarlett - VvV (ideally the single-card version, but I don't have her!)
5. Snake eyes - VvV with Timber, although I'm often drawn to the Ninja Lightning one.
6. Stalker - VvV
7. Hawk (aka General Abernathy, aka Tomahawk) - VvV (might use a comic pack/'86 combo in stories though)
8. Cobra Commander - ARAH version that came with Chameleon
9. Destro - gold-head Despoiler pilot
10. Storm Shadow - VvV (mail-in for when he's a good guy)
11. Major Bludd - RAH Chinese exclusive (I don't have the DTC one yet)
12. Baroness - VvV single card
13. Zartan - comic pack
14. Zarana - comic pack (because I don't have the Spy Troops version yet)
15. Flint - comic pack
16. Gung Ho - VvV (o-ring)
17. Lady Jaye - comic pack
18. Dr MindBender - VvV
19. Xamot and Tomax - original (would be the 6-pack ones if their suits were mirror-image)
20. Clutch - Mega Marines (really. I like the head sculpt, and the armour on the sculpt is cool. DEFINITELY needs recolouring though. I might pick the Desert Coyote's Double Clutch if I had him)
And I'd just like to add comic pack Firefly to the list, since he's had quite a few variations himself!