This would depend if you want to go all the way back to 1869. If you do, Yale has the most with 18 followed by Princeton with 17 and then Notre Dame with 13. If you want to go back only to 1936, when the Media Polls came out, then Notre Dame is the leader with 9.
Princton
Alabama
According to wikipedia. Princeton has the most titles with 28.
usc has 20 jk
SEC
Mount Union with 10 (1993, 1996, 1997, 1998, 2000, 2001, 2002, 2005, 2006, 2008).
Alabama
The University of Alabama Crimson Tide
The Michigan Wolverines have won a total of 11 national championships in college football. Their titles were claimed in various years, with the most recent one being in 1997. In addition to football, Michigan has also had success in other sports, but the 11 national titles specifically refer to their football achievements.
Manchester City with 7 second Division Titles
In college football, FSU has two National Championships. One in 1993 over Nebraska and one in 1999 over Virginia Tech.
The University of Michigan football team claims a total of 11 national championships, with the titles spanning several decades, with the most recent championship win in 1997. These titles are based on various polls and rankings, as the official NCAA does not award championships in football. Michigan is recognized as one of the most successful programs in college football history.