John Gagliardi, the current coach of Carroll College in Montana is the all time leader with 461 wins, with 437 of the wins coming at Division III St. John's University in Minnesota. Second is Eddie Robinson the legendary coach of Grambling State University with 408 wins, which is the Division I record.
Some of the winningest college football coaches of all-time are Eddie Robinson, Joe Paterno, Bobby Bowden, Woody Hayes, Bo Schembechler, Lloyd Carr, Lou Holtz, Bear Bryant, Pete Carroll and Tom Osborne.
These were the numbers at the end of the 2008 season
John Gagliardi - 461 wins
Eddie Robinson - 408 wins
Joe Paterno - 383 wins
Bobby Bowden - 382 wins
Amos Alonzo Stagg - 329 wins
Paul W. "Bear" Bryant - 323 wins
Glenn Scobey "Pop" Warner - 318