I would take the highest ranked conference winner.
So only conference champions should be allowed to play in the NC game?
OK, consider this likely scenario: Bama drops their game to LSU, and UGA or Florida drops another game but beats LSU in the SEC title game; KU or Mizzou wins the Big 12 title game; Wake or VT win the ACC title game; the winner of the OSU-Penn State game loses another game.
So we have as conference champs:
ACC: Wake or VT, who will have at least 2 losses
Big East: USF with 1 loss
Big 10: Penn State with 1 loss or OSU with 2 losses
Pac-10: USC with 1 loss
Big 12: Misery or KU, who will have at least 2 losses
Meanwhile, OU, Bama, TT or OSU, and UT all end up with 1 loss, but none of these teams won their conference.
So who's in your NC game? USC I'll give you. But there's no way that USF or Penn State would be deserving over a 1-loss OU, Bama, or Texas team. Even if Ohio State wins out I wouldn't take them over a 1-loss OU or Bama team.