I agree about the ACC. They have some historically strong programs and these things run in cycles. The Big East, however, lost their strong football programs to the ACC (Miami, BC, Va Tech). The Mountain West/old WAC (as opposed to the current WAC) has been a major football conference for a long time, much longer than the ACC or certainly the Big East - which wasn't even a conference. - Wyoming was a national power in the 60's (Texas took coach Fred Akers from there) - AF got some top 10 rankings (though they weren't in the conference then). Remember, the PAC-8 became the PAC-10 by stealing Arizona and Az St. In the late 80's early 90's or so, the MtnWest/WAC had 5 teams in the top 25 for a week or two and the PAC-10 had none - BYU (who won a national championship), AF, Utah, CSU, and New Mexico. A lot of the kids are recruited from California, so the PAC-10 and MtnWest tend to cycle opposite each other (though of course AF is national and TCU is Texas).
Boise St. beat TCU last year in their BCS bowl.
Until the middle of this year, the last team to beat Alabama was Utah, which crushed them in the bowl game. (Also, I think Urban Meyer's Utah team was the best in the country that year - they were the biggest, strongest team in the country and should have gotten someone better than Pittsburg to prove it against. People think of non-BCS conferences doing it with speed and guile, but that Utah team was big.)
Yes, it's sad that New Mexico, CSU, and a couple of the others are so terrible and I don't think the MtnWest will ever have the depth that the ACC does - a far smaller population to draw recruits from. Historically, the current situation has been true a lot of the time. A couple really top teams and the rest far behind.