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The Oregon Ducks are not ranked second in the initial BCS standings. The Florida Gators have taken their spot.
Obviously, there will be calls for "SEC bias" here at having two SEC teams lined up in the top two slots in Alabama and Florida. But this is probably justified. Florida has beaten Texas A&M on the road and beaten a top-25 quality team in LSU at home. Oregon has beaten no one of that caliber. Florida has two big road wins against A&M and Tennessee. Oregon has yet to leave the Pacific Northwest (five of their first six games are at home, and their "road" game was at a neutral site).
The good news is that the Ducks will have a good shot to start making up ground by beating teams like Arizona State, Oregon State, Stanford, USC, and maybe USC or Arizona State again in the Pac-12 title game. If Alabama and Florida stay this high, one of them will knock the other out, so the Ducks should feel pretty comfortable that they control their own destiny.
The Oregon St. Beavers are currently eighth and also should feel pretty much like they're in control of their own destiny. The USC Trojans less so at 10th, but they will play Oregon and Notre Dame each and have a good shot at being the top one-loss team if they get that chance. The Stanford Cardinal are currently 20th and are probably thinking Rose Bowl or bust at this point.