Not quite in order, but I tried to think of figures I like to keep around:
1. BAT v1 (hey, the lower half alone made for a million Vipers! Hi-tech Cobra works for me, so a little Terminator in my GIJoe is okay)
2. Stalker v1.5 (vintage, but he looks great with all years' figures)
3. Iron Grenadier v1 (not too sci-fi, but a radically different shock trooper)
4. Airborne v1 (another vintage guy that, even with the light blue, looks great with newer figures)
5. Snake Eyes v1 (or any remold of it. V2 is iconic, but I just like the goggles/skimask look for a commando)
6. Cobra Officer v1 (love the mold, and it looks great as the Stinger driver too)
7. Firefly v1 (or most repaints; I don't shoot him much, but same as Stalker, he holds up over the years)
8. Major Bludd v1 (always liked this figure; he's had cool updates, but the original stands)
9. Viper v15 (the Viper Pit; nevermind the boots; better paint detailing than v1, and I'm not afraid to let it get beat up)
10. Cobra Trooper v1 (includes TBM customs; fill a scene with them and you can't go wrong. A much better "grunt" than Grunt)

Honorable Mention:
arctic Stalker (v2+v4 custom; if it snows, I'm usually taking a photo with him in it)
Zartan v1 (unusual, yet perfect look for a mysterious character)
Crimson Guard (I just like the look, and the TBM customs helped get them on the battlefield)
Cobra Commander v1.5 (some of his updates were cool, but this figure never gets put away)