Here's what the playoffs would look like if the top four teams were picked, regardless of conference championship status. The rankings used and listed are the BCS ones.
No. 1 Oklahoma (12-1) vs. No. 4 Alabama (12-1)
No. 1 Alabama (13-0) vs. No. 4 TCU (12-0)
No. 2 Texas (13-0) vs. No. 3 Cincinnati (12-0)
No. 2 Oregon (12-0) vs. No. 3 TCU (12-0)
No. 1 LSU (13-0) vs. No. 4 Stanford (11-1)
No. 2 Alabama (11-1) vs. No. 3 Oklahoma State (11-1)
2011 has both the best and worst of this world. On one hand, you're gifted the Alabama-Oklahoma State semifinal. And wouldn't it have been great last year if instead of all the griping, you could have just dumped Alabama and Oklahoma State into a stadium to settle who gets to go to the championship? On the other, you have the only (in my mind at least) real team put to the screws. That's No. 5 Oregon, which actually won the Pac-12, and beat Stanford by 23 points at Stanford, but is ranked one spot lower because the Ducks had the gall to play No. 1 LSU in the first game of the season.
And that's the main gripe with this system: it could encourage teams to avoid more difficult schedules. In the conference champion scenario, only conference play truly matters, so teams are encouraged to schedule to prepare their teams. But if you're just aiming for a top-four poll spot, you might as well schedule down in non-conference play because a non-conference loss can really hurt you.
The 2007 and 2009 playoffs would have been the same in either scenario.