The NCAA started recognizing championships in 1936. They did not name the champion, they just recognized who was named champion. If you count before 1936 to get the 11 and 12 that Alabama and Notre Dame have then you would have to count the 17 by princeton and the others by yale and so forth.
Yale has 18 titles since 1869. Princeton has 15, Notre Dame 11, Alabama 10
and... prior to the 1998 season, no team won any national championship. Instead, national championships were awarded to teams based on various subjective polls (AP, UPI, etc.) The Bowl Championship Series changed all that by establishing a "National Championship Game" (played between the two "best" teams), forcing a team to actuallywin the national championship, rather than being awarded the national championship based on the results of some poll of sportswriters or coaches. Admittedly, the BCS still has problems, and there have been at least 4 occasions (2001, 2003, 2004, and 2007 seasons) when there was some controversy over whether the two best teams got the chance to play in that national championship game. These problems will continue until Division 1-A institutes a real playoff system. Until that time, however, the BCS is far better than the previous systems in that it at least forces a team to win a national championship. That said, since the establishment of the BCS and the National Championship Game, LSU has won 2 of those National Championship Games (2003 and 2007 seasons), and no other team has accomplished this many National Championship Game wins.
this is a gotcha question... you knew that already though didn't you sharma?
also this is the kind of thing that can be googled... this answer came from:
http://wiki.answers.com/Q/Which_NCAA_Football_team_has_won_the_most_National_Championships_in_Modern_Football