Counting only regular season games between 1999 and 2013, the teams with the most wins are :
Overall - New England 171 of 224 (76%)*
NFC only - Green Bay 147 of 224 (65%)
*If not for their abysmal 2011 season, Indianapolis would be the leader.
Through the 2009 season, that is 104 by the 1905 team that was known as the Brooklyn Superbas. The most losses in a season the team has had since playing in Los Angeles is 99 by the 1992 team.
Chicago Cubs
San Francisco. It was formerly an NFL record for wins in a decade, but the Colts broke it last week.
The most losses by a team in NBA history was by the 1972-73 Philadelphia 76ers who had a regular season record of 9-73.
Rangers
Through the 2009 season, that is 104 by the 1905 team that was known as the Brooklyn Superbas. The most losses in a season the team has had since playing in Los Angeles is 99 by the 1992 team.
Patriots
colts
Through the 2008 season, the franchise record for wins in a season in 105 by the 1953 Brooklyn Dodgers. Since coming to LA in 1958, the most wins the team has had in a season is 102 in 1962 and 1974.
Chicago Cubs
The Miami Dolphins
49ers
The Indianapolis Colts had 128 regular season wins 1999-2009 (11 seasons, 72%)
Manchester city
Across the entire NCAA, a Division III team, Mount Union, has 208 wins, more than any other college program at any level. Mount Union is 208-9 since the start of the 1999 season with seven national championships. A Division II team, Grand Valley State, has won more games than any other program in any division which offers scholarships to players. Grand Valley State is 166-29 since the beginning of the 1999 season with four national championships.
San Fransisco '49ers
The English Premier League Team that was crowned the EPL champion for the 1999 and 2000 season was Manchester United while Arsenal were the runners-up.