Princeton has the most with 28. http://en.wikipedia.org/wiki/College_football_national_championships_in_NCAA_Division_I_FBS#National_championship_claims_by_school
Yale - 27 Championships.
which player won the most BCS championships
UCLA has won 11 NCAA mens championships. Tennessee has won 8 NCAA women's championships.
In "modern football" there are no black colleges. Ever heard of desegregation?