I like that computers are part of the BCS rankings. They're objective. That doesn't mean they're smart, though, since any computer ranking is only as smart as the people writing the ranking algorithm.
I'll pick on Jeff Sagarin, since his rankings are the best known and he's the most extreme with the Big 12. Here are the Big 12 teams in his BCS rankings:
2. Oklahoma State (10-0; AP#2)
6. Oklahoma (8-1; AP#5)
7. Kansas State (8-2; AP#16)
9. Baylor (6-3; AP#25)
12. Texas A&M (5-5; no AP votes)
13. Texas (6-3; AP#31)
17. Missouri (5-5; no AP votes)
26. Texas Tech (5-5; no AP votes)
28. Iowa State (5-4; no AP votes)
66. Kansas (2-8; no AP votes)
For reference, he has Michigan at #27 and his top ranked Big Ten team, Michigan State, is #22. In other words, he believes that 70% of the Big 12 has had a more impressive season than every single Big Ten team. Every Big 12 team but Kansas has been better than Wisconsin.
It seems like these rankings are far too kind to teams struggling in conferences that perform well in a few nonconference games. The Big 12 performed relatively well, granted, but here are all of their games against AQ conference teams:
Wins (6): Arizona (OSU), Florida State (OU), Miami (K-State), UCLA (Texas), Iowa (ISU), UConn (ISU) [note: they also had a few solid wins against TCU, Tulsa, etc.]
Losses (3): Arkansas (TAM), Arizona State (Missouri), Georgia Tech (Kansas)
This is a trivial thing to get worked up about, but these rankings make a big difference in determining who plays in BCS games and the championship game. Problems here can have major consequences.