As much as I hate to admit it, USC is the team of the decade with a record of 102-26, 6-1 in major bowls and 2 national titles.
Florida 100-30 4-1 in major bowls, 1-4 in others and 2 titles.
LSU 99-31, 4-0, 3-3, 2 titles.
Ohio State 102-25 4-3,1-2, 1 title.
Oklahoma 110-24, 2-5, 2-1 1 title.
Texas 110-19, 3-1, 4-2
Miami 92-33, 3-1, 2-3 1 title.
Georgia
Oregon
FSU
Va Tech
Alabama 89-50 1 title
Oregon St.
Michigan
Auburn 88-39 1-0, 5-3
Notre Dame
Tennessee
Ga Tech
UCLA
Cal
Penn St.
Iowa
Wisconsin
W. Virginia
Boston Col.
also Boise St. 112-17, 3-4 other bowls
These numbers are from the College Football Data Warehouse and converted by a renowned numbers genius who blogs on The Sporting News site, a defense atty, going by George_Tirebiter. He converted the top teams and I didn't have proper time in one sitting to pick the formula nor to tabulate. Very good site for stats though. He would know.