I don't think I could pick a Favorite Joe. I always liked Snake Eyes, but the comic ruined it for me, they spent too much time focusing on him. There were lost of Joes that had cool personalities (as per their file cards) but the figures sucked, or the comics didn't give them any air time! so how to choose!?!? Let's say this.....
As far as looking cool, my all Time Favorite had to be Falcon. Love the Beret! (and unlike Flint, hasbro made teh Beret look right on Falcon). The ONLY reason I hated Flint was the frakked up French Chef's hat they tried to pass of as a beret on the figure! If the figure looked like the comic version, we'd be good! (BTW, I LOVE the comic version that came with the 3packs! That's the way the V1 shoudl have looked!)
My Favorite as far as Character was definitely LowLight (read the V1 fileCard) and Mainframe was definitely second. I like the "old Crusty" guys! (Damn you Devils Due for killing him off...damn you to hell)
Favorite Cobra? Hmmmm....that's a hard one. Cobra has fractured into so many different organizatons in the past. In My JoeVerse, the coil, Zartan and the Dreadnoks and the Iron Grenadiers are their own seperate armies. They work together sometimes, but they are not under cobra! But as far as bad guys go, I like Wraith. (although they could have done sooooo much more with him) and Zartan. (because when push comes to shove, Zartan will kick your @$$...ask Serpentor, Zandar or Firefly!)
Favorite troops? Frag Vipers. The figures need updating, but I like the concept. As for looks, the night vipers get my vote hands down!