GameFAQs, run by CJayC, is where the beginnings of GAJ were. Its where most of the users of GAJ originate, and for most of us, its how we have found the boards.
The few boards which have had the most to do with GAJ are the GTA San Andreas Board, and the dead board for a little known Commodor 64 game called Jack Attack.
The former was the true beginnings of GAJ. It was where all the shit was being flung at by Jack Thompson, and where the most up to date JT stuff was being posted. It was also the original advertising spot for Jack Attack and then GAJ, since GTA was the one game that was always cited as destroying our kids's minds.
Jack Attack was the other forum, which has arguably had the most impact on GAJ. It was where GAJ was founded, and where all the original users found the Free Forum World GAJ.