Even if you take out Tom's counts and try another count, it still stands. I'm with ya in that I don't think LSU has 7 quality wins, Bama 6, etc. I would count quality wins as any team with 8+ wins.
LSU has wins over 10-2 Oregon, 10-2 Arkansas, 11-1 Alabama, and 9-3 West Virginia.
Alabama has wins over 9-3 Penn State and 10-2 Arkansas.
Oklahoma State has wins over Baylor (8-4 or 9-3), Texas (if they beat Baylor they're 8-4), 8-4 Tulsa, 10-2 Kansas State, and 8-4 or 9-3 ULL, plus 9-3 Oklahoma if they do indeed win out.
Boise State has wins over 11-2 Georgia and 8-4 Tulsa.
I think it's clear that LSU and OSU have the two best resumes, and that Bama's wins beat out Boise's wins. Bama's loss is also better than Boise's loss, if we need to look further.
The next level even looks better.
Virginia Tech has wins over 8-4 Virginia, 9-3 or 10-2 Arkansas State and 8-4 Georgia Tech. VT will also get a win over a 9-4 or 10-3 Clemson team. In fact, Virginia Tech might even have an argument over Bama... though at that point it really doesn't matter since they're fighting for #3, not #2.
Stanford has wins over 10-2 Southern Cal and will probably get one on 8-4 Notre Dame.
Stanford gets the advantage due to better loss, Virginia Tech has a better resume in general.
I'd rank 'em:
1. LSU (12-1)
2. Oklahoma State (11-1)
3. Alabama (11-1)
4. Virginia Tech (12-1)
5. Stanford (11-1)
6. Boise State (11-1)