This is probably a mess; so many teams are missing good victories and some of those that do have a bad loss (coughSouthCarolinacough). This is a first pass; let me hear where I'm wrong in the comments. I'm a bit under the weather, so my brain is not running on 100%.
3. Boise State
Oregon has been the most dominant, so it stays after a week off. Auburn passes Boise State as the Tigers accumulate good wins and Boise's schedule goes to crap. LSU is undefeated still, and it passes TCU thanks to the Frogs' one good win (Oregon State) losing value by the week.
7. Michigan State
Oklahoma's win over FSU looks better and better, but it has more close scrapes than LSU does. I think I might need Michigan State higher. Iowa has better measureables than Arizona does, but the head-to-head result holds serve for now. Alabama's profile took a hit with losses for South Carolina, Arkansas, and Florida this weekend.
12. Ohio State
15. Florida State
The Badgers finally beat someone of consequence, and that someone takes up shop behind them. Utah still hasn't beaten anyone worth talking about, but the Utes are very efficient. Did I push Nebraska too far down? FSU's defense is the reason for its resurgence this season.
18. Oklahoma State
19. South Carolina
20. Mississippi State
Stanford has no showcase wins yet. Missouri doesn't either, but its done almost everything you could ask for. Oklahoma State is wobbly but undefeated. I think I might be too generous to South Carolina. News flash in case you haven't noticed: Mississippi State's defense is for real.
21. West Virginia
24. Virginia Tech
25. Miami (FL)
Here's where I start getting to teams that I don't feel good about ranking. You've got the lack of good wins (West Virginia, Arkansas), bad losses (Texas, VT) and a combination thereof (Miami). Any suggestions for replacements?