A few notes before I put down what I find:

A. Cam Newton has come closest in this century, winning the College title and losing the SB

B. Tom Brady was on the Michigan college title team (shared)...but Brian Griese was the QB on that team. Brady only threw 15 passes all season.

C. Peyton Manning's Tennessee team won the college title...the year AFTER he left with Tee Martin at QB.

D. Troy Aikman was a part time QB on the 1985 Oklahoma title team...but the primary QB that year was Jamelle Holloway, a wishbone QB. It was because of that system that Aikman transferred. While Aikman played more than Brady did on a title team, he was still not the primary starter.

E. Steve Young is like Peyton Manning....his team, BYU, won the title the year after he left under Robbie Bosco at QB.

F. Bernie Kosar won a title at Miami, but, as we know, he came up short 3 times when trying to get to the SB.

G. Ken Stabler was a backup QB on the 1965 Alabama National Champ, but he only threw 11 passes that year (Steve Sloan was primary QB)

So. Here is what we have: For any Super Bowl winning QB, there are two that also started for a College National Champion. Just a couple of Joes:

Joe Namath for the 1964 Alabama national champs

Joe Montana for the 1977 Notre Dame national champs.

In fact, going back to Pre Super Bowl times, I do not find a single other QB that won both an NFL/AFL title and a national championship. Names like Otto Graham, Sammy Baugh, Bob Waterfield, Bobby Layne, Van Brocklin, etc. etc. No NFL champion QB ever won a national title other than the two Joes.

Now, in the future a few guys still do have a chance: Newton, Jamies Winston, and I guess you could count guys like AJ McCarron or even Cardale Jones.