Using the SEC as a reference point, I think the Big XII is better top to bottom than every other conference, and this is a "body of work" comparison over the last several years.
There are more good programs in the SEC and Big XII than there are in any other conference. Nebraska and Texas A&M are down this year, but have traditionally fielded excellent football teams. Oklahoma, Texas, Colorado and Mizzou round out the top six. I think you'd be hard pressed to find six such programs in any other conference, except the SEC. The Pac-10 has USC, Cal, Oregon and UCLA. All good programs, each with their own troubles this year, but there is a significant drop off after those four.
The Big 10 has Michigan, Ohio State, Penn State and Wisconsin. Again, significant drop offs after those four. The ACC has Florida State, Virginia Tech, Boston College and Miami. Who has shown consistency after those four? Georgia Tech gets honorable mention.
The Big East is basically West Virginia's playground now.
None of the other BCS conferences can hold a candle to the SEC. The current top tier is LSU, Georgia, Florida and Auburn. The middle tier is Tennessee, Arkansas, South Carolina and Alabama (by a nose). The lower tier, MSU, Ole Miss, Kentucky and Vandy can play with and probably beat the middle tiers of any of the other conferences.
Over a consistent, body of work basis, the SEC Champ and the Big XII Champ would represent the best of the best, with occasional good runs made by the top teams from the other conferences.
JMO.