Princeton claims 28 national championships since 1869, the first season of College Football.
However, since 1936 (when the AP Poll began), both Alabama and Notre Dame are tied with 8 consensus titles.
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The Big 12, SEC, and ACC have conference championship games; the PAC 10, Big East, and Big 10 do not. I found the answer here: http://www.usatoday.com/sports/college/football/2007-10-18-bcs-q-and-a_N.htm
this isn't all but there is the SEC, the PAC-10, the MAC, the BIG-10, the ACC, the WAC and a bunch more.