UCLA - 100 Championships
The University of Michigan has the most with 11 national championships the last in 1997. GO BLUE
Stanford with 540
Depends on which sport or sports you are asking about.
LSU Men and Women have a combined 64 national championships as of spring 2007. That is, by far, the most by an SEC school.
116 national championships since 1895 in football. However most teams don't count their national championship pre ww2!
The UCLA Lady Bruins have won the most National Championships in Collegiate Fastpitch Softball...I believe they have won 25 or 26 National Championships.
Arkansas Razorbacks 42 national championships in track
The Alabama Crimson Tide with 14
Princeton With 26 National Championships.