http://football.stassen.com/cgi-bin/records/calc-wp.pl?start=1869&end=2007&rpct=30&min=5&se=on&by=Win+Pct
The University of Michigan is the most winningest football program in the history of the NCAA.
Tubby Smith
Bob Knight with 902 wins.
Duke
Notre Dame combined football and basketball and I believe Syracuse is 2nd.
Florida, Michigan
notre dame
Pat Summitt is the all-time winningest coach in NCAA basketball history, men or women, in any division.
three
football- LSU Basketball- Kansas
Alabama
arkansas' John McDonnald