I'm only old enough to remember the first cartoon series..
I have to say though as a kid I always rooted for Cobra, just because the Joes were such goody goody nit wit phoneys and didn't deserve to win all the time. That and they always won in the stupidest most lame ways possible, ususaly prompting me to yell "oh come oooon!" at the tv at the end of each episode.
I felt the same for the Transformers too. Couldn't stand the autobots, and wanted the decepticons to win.
Guess I'm not a goody goody and tend to like the underdog.

That or maybe I'm just evil