I'm surprised; I thought Snake Eyes would be the overwhelming Joe-of-choice. Glad to see the responses are a bit more varied than I expected.
Anyway, my favorite Joe is Jinx.
I know she only ever had a really big role in the animated movie, but I loved that thing when I was a kid. Would watch it over and over again with my brother, so much so that I had misremembered that she actually had a big part on the Sunbow television show. After looking it up when A Real American Hero
began airing recently on The Hub, though, it turns out she didn't even appear once on the darn show!
But I always liked her shtick: martial artist in all red who fought better when blinded. She kind of reminded me of another favorite character of mine, I guess.
And now for a nostalgic story: At the time of the film, Hasbro had this deal where you could mail away for Jinx and I believe Quick Kick if you sent in a certain number of proofs of purchase. My mother did this for my brother and me once before for that mail-away camera Transformer trio, but we never received them. After waiting several months for our Jinx and Quick Kick figure, my mother, upset over getting gypped by Hasbro once again, along with seeing how upset I was--not being able to get my very own Jinx figure--began her own letter-writing campaign to Hasbro. A few weeks later, not only did we receive our Jinx and Quick Kick figures, but we received two of each, two of those "You as a Joe" figures that they made, and several B.A.T.s to make up for my mother's inconvenience, along with a letter of apology. Very cool of Hasbro, I must say. Yeah... Good times, good times...
Oh, and my favorite member of Cobra: Probably Destro,
although I really loved my Serpentor action figure with his included flying chariot when I was a kid.