This is a hard choice because there are really great villains. I mean look at the years 1983 through 1987
Cobra Commander
Destro
Major Bludd
HISS Driver
Baroness
Storm Shadow
Firefly
Wild Weasel
Copperhead
Zartan
Scrap Iron
Stinger Driver
The Crimson Guard Commanders - Tomax and Xamot
Crimson Guard
Torch
Ripper
Buzzer
Monkeywrench
Zarana
Zandar
Thrasher
Serpentor
Big Boa
Croc Master
Raptor
Zanzibar
Battle Armor Cobra Commader (Crimson Guard)
Techno Viper
Golobulus
Nemesis Enforcer
Cobra La Royal Guard
BUT, G.I. Joe, at least among my friends, was responsible for the big ninja craze of the 80's all because of Snake Eyes. As cool as all of the COBRA characters are, Snake Eyes is the defining character. If they were to do a Masterpiece collection like Takara did with Transformers, the first figure would be Snake Eyes in my opinion. Just like Optimus Prime for Transformers, Snake Eyes is the Joe, so decisions, decisions.
Oh, who am I kidding, I am COBRA Command through and through.