Here’s an interesting Wiki article on the origins of American football at colleges in the US and Canada:
http://en.wikipedia.org/wiki/College_football
Note the colleges that were winning early (1869-1900) “national” championships:
http://en.wikipedia.org/wiki/College_football_national_championships_in_NCAA_Division_I_FBS
According to some claims, Princeton and Yale have the most championships historically (more than ND), but almost all of them were from that early period.