As of the 2013 season, the College Football team that has the best winning percentage in Division 1 is Old Dominion with a winning percentage of .767. Old Dominion has only played 60 games in Division 1 though.
Notre Dame is 2nd with a percentage of .733
Michigan is 3rd with a percentage of .732
49ers
Kentucky (.758), UNC (.738), Kansas (.713), UCLA (.697), Duke (.697), Syracuse (.685)... in that order.
Tampa bay rays
Assuming that the 2 represents ties, the winning percentage is .619 Assuming that the 7 represents ties, the winning percentage is .738
The 95-96 Chicago Bulls. They won 87 of their 100 games ( including playoffs). This team holds the NBA record for best winning percentage at .878.
North Dakota State University Bison
Michigan
1) Notre Dame-.74721 2) Michigan-.73981
University of Idaho .362 winning percentage (Kansas State has most all-time losses.)
49ers
NY Mets
New york yankees
alabama, lsu
Boise State 112 wins with a .868 winning percentage
Kentucky (.758), UNC (.738), Kansas (.713), UCLA (.697), Duke (.697), Syracuse (.685)... in that order.
Through the 2010 season, it's the Chicago Bears. They have a record of 704-512-42 for a winning percentage of .579.
Manchester United