The Alabama Crimson Tide have won the most NCAA Football Titles
The UCLA Bruins have won the most NCAA Basketball Titles
The USC Trojans have won the most NCAA Baseball Titles
In Women's NCAA Basketball the Connecticut Lady Huskies have the most NCAA Basketball Titles
Two schools have won NCAA national championships in football, baseball, and men's basketball:
Jacksonville State University (NCAA Division II)
Men's Basketball (1985)
Baseball (1990, 1991)
Football (1992)
University of Wisconsin-Whitewater (NCAA Division III)
Men's Basketball (1984, 1989)
Baseball (2005)
Football (2007, 2009, 2010)
Note 1: The NCAA does not officially sanction a football national championship in FBS / Division I
Note 2: Jacksonville State now competes at FCS / Division I
California (Football - 1920, 1921, 1922, 1937; Basketball - 1959; Baseball - 1947, 1957)
Michigan (Football - 1901, 1902, 1903, 1904, 1918, 1923, 1932, 1933, 1948, 1997; Basketball - 1997; Baseball - 1953, 1962)
Ohio State (Football - 1942, 1954, 1957, 1961, 1968, 1970, 2002; Basketball - 1960; Baseball - 1966)
Stanford (Football - 1926; Basketball - 1942; Baseball - 1987, 1988)
University of Kentucky
For the major sports, Alabama for football, UCLA for basketball, and LSU and South Carolina for baseball
1 championships 6 titles mostly played in a fieastea bowl and rose and sugar
Football, basketball and baseball
I don't know the complete list, but I do know that Michigan State was the first D-1 university to win two championships in both basketball and football. Florida is another one.
Two NAIA baseball championships (1977, 1979), and one in men's basketball (1986).
Maryland
No Alabama football coaches have won national championships.
11 NATIONAL CHAMPIONSHIPS
Alabama's Basketball team has 0 National Championships
The UConn men's basketball team has won 2 national championships coming in 1999 and 2004. The UConn women's basketball team has won 6 national championships. The Huskies won the 2009 national championship in April.
The University of North Carolina does not have any national championships in football.