I set these Conferences up several years ago to maximize traditional rivalries. Each team plays 12 Games. The 10-team conferences play a 9 game round robin, except for the Independence Conference, which only plays 4 conference games. The 12-team conferences play an 8 game conference slate, with various amounts of protected games, depending on the conference. Every conference has a Championship Game. After teams play a traditional (pre-BCS/Bowl Alliance/Bowl Coalition) the #1 and #2 teams in the country are selected to play in the National Championship Game. The 20 teams not listed would ether drop down to FCS or drop Football. Looking back, I probably would've included Buffalo, Nevada, and Lousiana at the expense of Ball State, San Jose State, and Utah State, respectively.

ACC
Boston College
Maryland
Virginia
Wake Forest
Duke
North Carolina
North Carolina State
Clemson
Georgia Tech
Florida State

Big 10
Ohio State
Michigan
Michigan State
Indiana
Purdue
Northwestern
Illinois
Wisconsin
Minnesota
Iowa

SEC
Florida
Georgia
South Carolina
Tennessee
Vanderbilt
Kentucky
Auburn
Alabama
Mississippi
Mississippi State
LSU
Arkansas

Big 12
Iowa State
Nebraska
Colorado
Kansas
Kansas State
Missouri
Oklahoma
Oklahoma State
Texas
Texas Tech
Texas A&M
Baylor

PAC-10
Washington
Washington State
Oregon
Oregon State
Stanford
Cal
USC
UCLA
Arizona State
Arizona

Independence (Conference-in-Name-Only for the sake of a Championship Game)
Army
Navy
Air Force
Penn State
Notre Dame
Miami
BYU
Rice
Temple
Hawaii

Big East
Connecticut
Syracuse
Rutgers
Pittsburgh
West Virginia
Cincinnati
Louisville
Virginia Tech
Memphis
Houston
Central Florida
South Florida

WAC
Tulsa
TCU
SMU
New Mexico
Colorado State
Wyoming
Boise State
Utah
UNLV
San Jose State
Fresno State
San Diego State

Conference-USA
Northern Illinois
Marshall
Utah State
East Carolina
Florida Atlantic
Florida International
North Texas
UTEP
UTSA
Louisiana Tech
Tulane
Southern Mississippi

MAC
Kent State
Akron
Ohio
Miami (OH)
Toledo
Kent State
Eastern Michigan
Central Michigan
Western Michigan
Ball State

Major Bowl Games (There are others that I won't list. Ideally ~50% of team would be bowl-eligible)
One of the 5 At Large Teams must be a champion of the WAC, Conference-USA, or MAC.

Rose Bowl
Big 10 Champ vs PAC-10 Champ

Orange Bowl
Big East Champ vs At Large

Sugar Bowl
Big 12 Champ vs SEC Champ

Peach Bowl
ACC Champ vs At Large

Cotton Bowl
Independence Champ vs At Large

Fiesta Bowl
At Large vs At Large