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
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.
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
Oakland Raiders
bates college
Fighting Irish 95. Ohio State and USC 78.
notre dame
Michigan
As of the start of the 2007 season, the Division 1-AA team with the most all time wins was Yale with 839.
University of Idaho .362 winning percentage (Kansas State has most all-time losses.)
If you are asking about college football, I believe all fifty states have at least one college with a football team, and some have many more than one. If you are asking about professional football, there are a number of states that do not have a team at this time: among them are Maine, Mississippi, Alaska, Hawaii, Vermont, and North Dakota.
The Alabama Crimson Tide.