Depends on what you looking for, since the FCS and FBS play a different amount of games per year you should be asking what College Football team has the highest winning percentage?
Answer would be Boise State 0.873 (124-18)
If you just want the highest number of wins then that would be the Montana Grizzlies with a percentage of 0.828 (126-26)
Number of wins and losses are being pulled from the 2000 - 2010 seasons
Overall The University of Montana has won 119 games since 2000 as of their 12-12-09 win over Appalachian State. One game remains for the Grizzlies in the NCAA Div I-AA FCS National Championship game 12-18-09 to attempt to push their wins to 120. Montana has a win percentage of .844 with a record of 119-22 since 2000.
In the BCS The Oklahoma Sooners have won the most with 104 wins and Boise State is next with 103 wins.
Notre Dame with 790.
University of Southern California
All-Time College Basketball Team With Most Wins up til 08-09 season* University of Kentucky with a record of 1988 wins and 635 lossesAll-Time College Football Team With Most Wins 1869-2008* Michigan with a record of 872-295-36
maybe this will help ...http://www.secsportsfan.com/top-all-time-ncaa-college-football-national-championship-conference.html
Fighting Irish 95. Ohio State and USC 78.
The Alabama Crimson Tide.