I just want to preface this letting you know I don't have a favorite college football team and the BCS is the reason.  Michigan State is currently being screwed by the system, just like countless other teams have been. Regardless of which team you cheer for, the fact that a computer decides on who will be in the National Championship game is absurd.  Why does the BCS suck so bad?  According to ripbcs.com

The BCS is a tournament system that includes only two teams.  That alone should disqualify it.
But the manner in which those two teams are selected is indefensible.
The process of selecting the two best teams for the BCS game has resulted in controversy almost every season of its existence.
The fact that 2 polls and a computer are used to determine a sports championship is idiotic.  And now teams are jumping conferences to increase their chance to win a championship, evidenced by TCU's recent decision to jump to the Big East.  The T in TCU stands for Texas.  Now the BCS is messing with geography and America is worse off for it.  Which is why Congress is getting involved, which makes me worry even more.
What's the solution?  I really don't know.  A playoff series of some sort, but I'm not the man to figure out the specifics of the thing.    But until someone does, and all D-1 college football teams have a fair chance at the National Championship, I'll remain a passive college football watcher feeling bad for teams that didn't lose but still can't win this...