No, not in the BCS era. I think it happened a lot in the AP system when you can pick who you wanted to play. That system was retarded.
There has NEVER been a Big 5 bowl game (Rose, Cotton, Sugar, Fiesta, Orange) pitting 2 teams from the same conference...let alone for the NC title. Also the bowl games sent out invites to teams in their geographic area to come play. Funny thing is if the BCS was around 15 years ago UF wouldnt have gotten a chance to earn a NC title in 96 with the rematch W over fsu. It would of been #1 FSU vs #2 ASU
I actually like the previous system. The BCS was implemented to stop situations like 96 and 97. The true problem with the system was the Rose Bowl took away the Pac 10 and Big 10 champ every year. That is where the problem laid. It was easy to get #1 and #2 to play in the Orange, Sugar, or Orange Bowl if they werent the Big 10/Pac 10 champ.