It does not matter in the BCS standings because the AP pulled out after last season, citing conflict-of-interest concerns. But the AP will crown its own champion following the season, which may not be the same champion anointed by the BCS.
Computers factor not only how a team's opponents perform each week, but also those opponents' strength of schedule. For example, today's Notre Dame-Tennessee game is important in the national title race. If the Fighting Irish were to lose to a 3-4 team, USC's win over them would be diminished in the eyes of the computers.
The computer formulas do not account for a team's ranking in the human polls. Instead, the computer formulas consider an opponent's record. So beating Michigan, ranked 23rd in the USA Today coaches' poll with a 6-3 record, does not mean as much as beating Boise State, which is unranked but has a 6-2 mark.
Finishing first or second is worthy of the same celebration because it means a berth in the Rose Bowl. There is not always shame in finishing third. Two years ago, USC, ranked first in both human polls, was ranked third in the BCS standings and was eventually crowned national champ by the AP.
Humans are often at fault, too. Two years ago, Oklahoma lost in the Big 12 title game to Kansas State, 35-7. The Sooners still received two first-place votes in the next Associated Press poll and eight in the USA Today coaches' poll, helping vault them past USC, the team ranked first in both human polls.