For major BCS conference teams, the Texas Longhorns have the best record at 103-25 through the 2008 season. Boise State, a Division I school not in a BCS conference is 102-24. If you want to know the best record regardless of the level, by far, the best College Football record in the past 10 years belongs to the Division III Mount Union Purple Raiders with 111 wins and only 3 losses.
Montana Grizzlies with 119 wins as of their December 12, 2009 semifinal win over Appalachian State. This trumps all FCS and FBS teams with the nearest FCS team. Montana has a win percentage of .844 with 119 wins and only 22 losses since 2000.
USC Trojans
Best College football record over the last 5 years
The University of Michigan is the most winningest football program in the history of the NCAA.
florida
THE FLORIDA GATORS
the ACC
Boise State
Texas
Alabama
74 in the last 50 years
Nebraska Cornhuskers
Boise State University in Idaho has become the unlikely college football power over the last 10 years.