Alabama is ranked number one and Oregon number two at the moment. It appears that they are the two best teams, but there is a lot of football to be played. I'll really be impressed with Oregon if they make it through their PAC-12 schedule undefeated, because the PAC-12 is loaded with good teams. Alabama, on the other hand, has in my opinion only one really tough game in the regular season, and that is at LSU.
The best college football team is the one that wins the BCS Championship Game. I'm thinking Alabama will get there. The other team could be LSU again, Florida State, or Oregon. If USC beats Oregon in the regular season and wins the PAC-12 Championship Game, USC takes Oregon's place in the mix. I don't really see any other teams with a shot.