If the Pac-10 absorbed the Big 12 in the manner described in this article, I could see the following domino effect...
Kentucky (yes, Kentucky)
Are all of these changes likely? No. I'd put my money on the Big Ten trying to grab some Big East schools before it scoops up 4 teams from the Big 12. However, I also don't see Kansas and Kansas State floating aimlessly without a conference, either.
The question really remains as to what happens with the Big East, ACC, and SEC if the Pac-10 and Big Ten start maneuvering (which causes the collapse of the Big 12).
I could see the basketball schools of the ACC combining with the basketball-heavy Big East and creating a juggernaut for basketball, with the side effect of also creating a 'feature' 16-team football conference (the other Big East non-football schools would likely have to form their own basketball conference). Once it started seeing the maneuverings towards four power conferences, I would bet good money Notre Dame finally sees the light and joins a football conference, though possibly with special treatment (perhaps a deal that it can play fewer conference games - or force the Big East to only play 7 conference games so it can maintain its traditional rivalries for the other 5 games).
The SEC would obviously want to maneuver as well, perhaps by shoring up the support in states it's already located in, with the obvious side effect of strengthening its football glory (who wouldn't want Clemson, Georgia Tech, Florida State, and Miami from the ACC- schools that all make more geographic sense, too). South Florida, a geographic oddity in the Big East, would finally find a home in the Southeast this way as well, with the Tampa market secure. This would force Tennessee and Vandy into the West, which isn't too crazy.
I think from there, the 4 power 16-team conferences could arrange some sort of +1 Championship that wouldn't disrupt the college football bowl tradition too much. I also think it'd make sense for conferences to only do 7- or 8-game conference football schedules. In an 8-game case, perhaps a 'permanent rival' situation like the SEC does for schedule balancing could be used, or maybe even a game vs. the team that finished in the same divisional position the year before (I also wouldn't be terribly surprised if one conference eventually tried splitting their teams into 4 divisions with a conference semi-final round + championship at some point, though I doubt it'd happen right away).
The regular season would still matter, as we're still looking at a situation where only 4-8 teams get a shot out of 64 at the national championship, and the slight pressure away from perfection would make for juicier non-conference match-ups to battle-test the contenders.
Yes, this still screws the teams like TCU, Utah, Boise State, etc., but I have a feeling those teams (save for possibly Utah) are going to wind up screwed anyway. I'm not saying this 'Big 64' world is ideal - I'm saying it's a possibility, and an interesting one at that. It's still always possible that the remaining FBS teams would form their own super-conferences, with a clause that the '+1 format' be required to take the 4 highest-ranked champions (i.e. an upset in one of the power conference championships could see a Boise State or TCU still sneak into what would more or less be a 4-team playoff).
[For those keeping score at home, Baylor and Iowa State are the teams who wind up screwed among the current power conferences.]
Here's a quick little PaintShop image I put together on what the conferences would look like:
Red = PAC-16
Purple = BIG 16
Teal = EAST 16
Blue = SOUTHEAST 16
Possible other configurations:
San Diego State
Conference USA would have to replace SMU/Houston, and would likely do so with a Sun Belt team (Troy or Middle Tennessee State makes the most sense from a sporting perspective; North Texas or one of the Florida schools from a market perspective).Or they could perhaps take Louisiana Tech away from the WAC.
The WAC could also possibly pick up a Sun Belt team, become smaller, or be the waiting conference for a lot of schools from western states that are slowly maneuvering their way up to FBS football.
I think that with a BCS clause that demands the 4 highest-ranked conference champions participate the 'Mountain West/12' could still be relevant, and Conference USA could occasionally make some noise. The lower conferences (Mountain West/12, Conference USA, WAC, MAC, and Sun Belt) could also try to make arrangements to pit their champions against each other in protest, similar to what they tried to arrange a few years back in the Liberty Bowl.
Anyways, those are just some ideas. *shrug*