First of all, I recognize that technically non- automatic qualifying schools are also in BCS conferences, but you know what I mean.
This is not just based on my own feelings, but rather a quantitative analysis involving four separate factors.
1) Athletic performance This is NOT just for football
2) Academic/Research reputation
3) Athletic department budget/revenue (not always available for private schools, but there are educated guesses)
4) Room for growth/size of market
With that being said, here's what I came up with. I was surprised at some of the stuff I came up with, particularly in terms of the large debt that some teams have.
1) Texas Christian University
2) University of Utah
3) University of New Mexico
4) Brigham Young University
5) University of Hawaii
6) University of Central Florida
7) University of Houston
8) San Diego State University
9) Boise State University
10) Villanova University