UCLA
Stanford with 540
Alabama
UCLA they have 101 national championships in all sports. (11 in basketball)
Depends on which sport or sports you are asking about.
Pac 10 with 400
UCLA with 100
LSU Men and Women have a combined 64 national championships as of spring 2007. That is, by far, the most by an SEC school.
UCLA
MIT?
Gators
The Texas Longhorns