How would a playoff system work for NCAA football?

There are 11 conferences and four independent teams. It would be difficult to have a 64 team field like in basketball. (Football is much more physically grueling than basketball is.) There would inevitably be some teams left out who feel that they should be there. For example, what if the runners up in the PAC 10, Big 10, Big 12, SEC, Big East, or ACC each had only one or two losses, on the year, and those were to top 25 teams, but the champion of the Conference USA or Sun Belt conference were undefeated. Who would be left out? This is a dilemma that I haven't heard anything about. What would be a fair way of deciding who gets to play in the playoffs and who stays home?