What college has won the most NCAA baseball national championships?

Won Most Championships

University of Southern California (USC) - 12 (1948, 1958, 1961, 1963, 1968, 1970, 1971, 1972, 1973, 1974, 1978, 1998.)
Louisiana State University (LSU) - 6 (1991, 1993, 1996, 1997, 2000, 2009.)
University of Texas - 6 (1949, 1950, 1975, 1983, 2002, 2005.)
Arizona State University (ASU) - 5 (1965, 1967, 1969, 1977, 1981.)

Southern California won 12. Here's all the National Champions and runner-ups:

Division I Baseball Champions
Year Champion Score Runner-Up
1947 California 8-7 Yale
1948 Southern California 9-2 Yale
1949 Texas 10-3 Wake Forest
1950 Texas 3-0 Washington St.
1951 Oklahoma 3-2 Tennessee
1952 Holy Cross 8-4 Missouri
1953 Michigan 7-5 Texas
1954 Missouri 4-1 Rollins
1955 Wake Forest 7-6 Western Mich.
1956 Minnesota 12-1 Arizona
1957 California 1-0 Penn St.
1958 Southern California 8-7Missouri
1959 Oklahoma St. 5-3 Arizona
1960 Minnesota 2-1 Southern California
1961 Southern California 1-0 Oklahoma St.
1962 Michigan 5-4 Santa Clara
1963 Southern California 5-2 Arizona
1964 Minnesota 5-1 Missouri
1965 Arizona St. 2-1 Ohio St.
1966 Ohio St. 8-2 Oklahoma St.
1967 Arizona St. 11-2 Houston
1968 Southern California 4-3 Southern Ill.
1969 Arizona St. 10-1 Tulsa
1970 Southern California 2-1 Florida St.
1971 Southern California 7-2 Southern Ill.
1972 Southern California 1-0 Arizona St.
1973 Southern California 4-3 Arizona St.
1974 Southern California 7-3 Miami (Fla.)
1975 Texas 5-1 South Carolina
1976 Arizona 7-1 Eastern Mich.
1977 Arizona St. 2-1 South Carolina
1978 Southern California 10-3 Arizona St.
1979 Cal St. Fullerton 2-1 Arkansas
1980 Arizona 5-3 Hawaii
1981 Arizona St. 7-4 Oklahoma St.
1982 Miami (Fla.) 9-3 Wichita St.
1983 Texas 4-3 Alabama
1984 Cal St. Fullerton 3-1 Texas
1985 Miami (Fla.) 10-6 Texas
1986 Arizona 10-2 Florida St.
1987 Stanford 9-5 Oklahoma St.
1988 Stanford 9-4 Arizona St.
1989 Wichita St. 5-3 Texas
1990 Georgia 2-1 Oklahoma St.
1991 LSU 6-3 Wichita St.
1992 Pepperdine 3-2 Cal St. Fullerton
1993 LSU 8-0 Wichita St.
1994 Oklahoma 13-5Georgia Tech
1995 Cal St. Fullerton 11-5 Southern California
1996 LSU 9-8 Miami (Fla.)
1997 LSU 13-6 Alabama
1998 Southern California 21-14 Arizona St.
1999 Miami (Fla.) 6-5 Florida St.
2000 LSU 6-5 Stanford
2001 Miami (Fla.) 12-1 Stanford
2002 Texas 12-6 South Carolina
2003 Rice (4-3, 3-8, 14-2)* Stanford
2004 Cal St. Fullerton (6-4, 3-2)* Texas
2005 Texas (4-2, 6-2)* Florida
2006 Oregon State (3-4, 11-7, 3-2)* North Carolina
2007 Oregon State (11-4, 9-3)* North Carolina
2008 Fresno State (6-7, 19-10, 6-1)* Georgia
2009 LSU (7-6, 1-5, 11-4)* Texas

* Beginning with the 2003 College World Series, the last two remaining teams (one from each of two 4-team double-elimination brackets) played a best-of-three series, with the first team to win two games claiming the national championship.