rcooke,
I don't have a best SOS site. They all vary tremendously. I would rather use the pollsters than any site that I have seen so far. But frankly it is not something I have particularly worried about.
Sagarin has LSU ranked 1st AFTER they won the National Championship and Va. Tech lost their bowl game. BEFORE the bowl games when records were IDENTICAL and LSU had won 48-7 he had Va. Tech #1. Lordy, I would hope that even Jeff Sagarin would have changed after the BCS games. All human polls had LSU ahead in last regular season poll.
In 2000 Miami and FSU each had one loss. FSU had an extra game because they got selected for the Kickoff Classic Game to start the season. Both teams had scheduled their normal 11 games. Each lost a game. Miami lost at Washington and FSU lost to MIAMI. All human polls had Miam ranked ahead in the last regular season poll. Washington had a better argument than FSU.
You said it all for 2003. I have not said the other computer selections were great either. I have not gone back and looked at their history, but in general they have been off the mark. Miami of Ohio.....better than USC in 2003. You would have to be smoking some real strong stuff to buy that. And the humans again, did not.
On 2006, you make my point for me. Yes the BCS corrected the Florida error because after the fiasco of 2003 computers no longer carry the weight they once did. The humans again had it right by putting Florida into the game instead of us getting a rematch. But had we been under the old system, it might have gone to Michigan. I would defer on that to a BCS guru.
As for 2007, and why LSU and UGA wound up #1 and #2. I guess LSU is obvious. UGA probably because they won their last 7 games against 6 bowl teams and all wins were by double digits. Nobody else was hotter during this period. But to get the clear answer you probably need to ask the 60 or so pollsters.
Look at the BCS era. In 98 the BCS loser fell to #3; in 00, the BCS loser fell to #5; in 01 the BCS loser fell to #8; in 03 USC won and LSU and OU swapped positions in the AP; in 04 the BCS loser fell to #3; in 07 the BCS loser fell to #5. It generally varies by how bad the loser lost by and how closely bunched other teams were, but it is hardly unusual for the loser to drop. Every team that was ranked ahead of UGA in the final rankings, less LSU lost. OU got trampled. Va. Tech lost to KU. Georgia was ranked ahead of USC in one poll and behind them in the other.
LSU and UGA may have set a precedence of ranking that high and not playing, but it is hardly new to see teams from the same conference ranked in the Top Ten even though they did not play each other.
2002 Ohio State#1 and Iowa #7. Had the Hawkeyes won their game they would have been at least #4...behind OSU, Miami and Georgia.
2006 Ohio State #2 and Wisconsin #7. Had a whole bunch of teams with the same or better record lost their bowl games in front of them, they too would have been higher.
2007 Mizzou #4 did not play #10 Texas; Kansas #7 did not play #8 OU or #10 Texas
Twelve team conferences are going to have times when highly ranked teams do not play each other if they don't happen to be in the Conference Championship Game. That is life in a conference that has 12 teams....no solution except to kick out someone. By the way it is also the way it happened twice recently in an 11 team conference.
Finally check out 2000. Your PAC 10 had 3 teams ranked in the Top 7. Washington #3, Oregon State #4 and Oregon #7. They were all 7-1 in conference play. The PAC 10 selected Washington to go to the Rose Bowl. How is that different that Georgia, Florida and Tennessee finishing in a tie in 2003 for the SEC East. Both issues were resolved according to the rules of the respective conferences. One difference. The three PAC 10 teams were Tri-Champs because they beat each other. LSU won the SEC and Georgia was the runner-up.
So whatever.