Game 1 - Cunningham. As mentioned earlier, I think Fouts was a product of his system. Cunningham created a system.
Game 2 - Duh. Montana. (Though I recognize that one can argue that he was a system quarterback, too.)
Game 3 - Baugh vs. Aikman. What an interesting matchup. I'm going Baugh just because I think he was a superior athlete and could create more ways to win.
Game 4 - Otto Graham is simply one of the best quarterbacks ever to play the game. His record as a starter was 114-20-4. He took his team to the championship game for ten straight years, winning seven. He had a career quarterback rating of 86.6 in an era when many starting QBs had ratings in the 60s. This guy was utterly amazing and easily deserves to move to the next round.
Game 5 - Favre and Tarkenton are the same player. Favre's records blow away everyone else's, but Tarkenton was the same way when he retired. Favre had a better arm, but Tarkenton was the original scrambler. I probably should take Favre here, but I'll go contrarian and take Tarkenton on the bet that he can win with both his arms and his legs.
Game 6 - Young in a walkaway. Simms was solid and Young was great.
Game 7 - I'm going to furtively avert my eyes and vote for Trent. Hey, Terry was a great quarterback and he had great teams. He also got benched at least once in his career. Trent worked his way steadily to the top and led one of the greatest offenses ever. Plus, he could lead block.
Game 8 - Where did this matchup come from? Geez. I would actually take Johnson here. Dude was seriously underrated and had a great arm.