Answer
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
See Also…
http://www.businessinsider.com/chart-of-the-day-who-has-the-winningest-college-football-program-since-2000-2011-1
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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.