The Commonwealth's Winningest Football Program
In the 21st Century, that title surprisingly belongs to the Bridgewater College Eagles.
According to Bridgewaterfootball.com, the Division III Eagles have posted the Commonwealth's best record since the start of the 2000 football season. Over that time Bridgewater has posted a record of 64-11 for a win percentage of .853. In second place is the Virginia Tech Hokies with a record of 57-19 for a win percentage of .750. The site has an interesting chart of all 23 of Virginia's football-playing schools and their records since the 2000 season.
Just for historical perspective, I looked up the all-time records of the Division I-A and I-AA schools to see how they compared. Virginia Tech was again the best posting an all-time win percentage of .593 through the 2004 season. Next best was JMU with a .540 win percentage, followed closely by UVA at .533. By contrast, Bridgewater College's all-time win percentage prior to the 2000 season was .277. That figure has increased to .356 thanks to Bridgewater's incredible run over the past 6 seasons, but that is still a painfully low total. In fact, a full third of Bridgewater's all-time victories have come in the past six seasons. That's pretty remarkable for a school that started playing football in 1899.