I'm actually going to put 2010 over 2009. The 2009 D was stout, but that offense was soooooo bad, unless the D set them up with a short field the chances of points were low. We lost games where the D gave up 16, 12, and 9 points. Taylor Martinez is super polarizing and turnover prone, but he added an element to the offense that 2009 couldn't compete with. If he'd have been able to stay healthy the 2010 squad wouldn't have won the title (Bo's teams mirrored his personality, too combustible for sustained elite performance), but their peak was higher.
For number 3 I'm going to go with the 2006 squad. Callahan gets a lot of hate, and the rails fell off in 2007, but we forget how close we were to truly turning the corner in 2006. There were still Solich players on that squad, players that were around the program when it was clicking. Shoulda-Coulda-Woulda, but they were a Terrance Nunn fumble away from beating a top 5 Texas team. Win that game and the whole history of the program could have changed. The Auburn bowl game is another we should have one. The D held Auburn under 200 yards, but the team had gave up two short fields after turnovers, and Auburn didn't make similar mistakes (I'm still mad at Andrew Shanle for dropping the handoff on a fake punt. It would have worked had he held on to it.).