UCLA's national championships: 103 NCAA Titles Men (71) Basketball (11): 1964, 1965, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1975, 1995
Golf (2): 1988, 2008
Gymnastics (2): 1984, 1987
Soccer (4): 1985, 1990, 1997, 2002
Swimming (1): 1982
Tennis (16): 1950, 1952, 1953, 1954, 1956, 1960, 1961, 1965, 1970, 1971, 1975, 1976 (tie with USC), 1979, 1982, 1984, 2005
Track & Field (8): 1956, 1966, 1971, 1972, 1973, 1978 (tie with UTEP), 1987, 1988
Volleyball (19): 1970, 1971, 1972, 1974, 1975, 1976, 1979, 1981, 1982, 1983, 1984, 1987, 1989, 1993, 1995, 1996, 1998, 2000, 2006
Water Polo (8): 1969, 1971, 1972, 1995, 1996, 1999, 2000, 2004
Women (32) Golf (2): 1991, 2004
Gymnastics (5): 1997, 2000, 2001, 2003, 2004
Softball (10): 1982, 1984, 1985, 1988, 1989, 1990, 1992, 1995, 1999, 2003, 2004
Tennis (1): 2008
Track & Field (5): 1982, 1983, 2000i, 2001i, 2004 (i = indoor)
Volleyball (3): 1984, 1990, 1991
Water Polo (6): 2001, 2003, 2005, 2006, 2007, 2008
Other championships (23) Men (8) Crew (2): 1972, 1973 (IRA Varsity Fours)
Football (1): 1954 (UPI)
Volleyball (5): 1953, 1955, 1956, 1965, 1967 (USVBA)
Women (15) Badminton (1): 1977 (AIAW)
Basketball (1): 1978 (AIAW)
Crew (1): 1974 (AIAW)
Golf (1): 1971 (DGWS)
Softball (1): 1978 (AIAW)
Tennis (1): 1981 (AIAW)
Track & Field (2): 1975, 1977 (AIAW)
Volleyball (3): 1971 (DGWS); 1974, 1975 (AIAW)
Water Polo (4): 1996, 1997, 1998, 2000
Total: 126 championships
And as a point of reference, here's Stanford's national championships:
Stanford's national championships: 95 NCAA Titles Men (58) Baseball (2): 1987, 1988
Basketball (1): 1942
Cross Country (4): 1996, 1997, 2002, 2003
Golf (8): 1938, 1939, 1941, 1942, 1946, 1953, 1994, 2007
Gymnastics (3): 1992, 1993, 1995
Swimming (8): 1967, 1985, 1986, 1987, 1992, 1993, 1994, 1998
Tennis (17): 1973, 1974, 1977, 1978, 1980, 1981, 1983, 1986, 1988, 1989, 1990, 1992, 1995, 1996, 1997, 1998, 2000
Track & Field (4): 1925, 1928, 1934, 2000
Volleyball (1): 1997
Water Polo (10): 1976, 1978, 1980, 1981, 1985, 1986, 1994, 1995, 2001, 2002
Women (37) Basketball (2): 1990, 1992
Cross Country (5): 1996, 2003, 2005, 2006, 2007
Swimming (8): 1983, 1989, 1992, 1993, 1994, 1995, 1996, 1998
Tennis (15): 1982, 1984, 1986, 1987, 1988, 1989, 1990, 1991, 1997, 1999, 2001, 2002, 2004, 2005, 2006
Volleyball (6): 1992, 1994, 1996, 1997, 2001, 2004
Water Polo (1): 2002
Other championships (11) Men (6) Basketball (2): 1937 (Helms Athletic Foundation), 1938 (Helms)
Football (2): 1926 (Dickinson System), 1940 (Helms)
Tennis (1): 1942
Water Polo (1): 1963
Women (4) Synchronized Swimming (2): 1998, 1999 (I am not making this up. Really.)
Swimming (1): 1980 (AIAW)
Tennis (1): 1978 (AIAW)
Co-ed (1) Sailing (1): 1997 (I am not making this one up either.)
Total: 106 championships
And here's USC's titles.
USC's national championships: 86 NCAA Titles Men (73) Baseball (12): 1948, 1958, 1961, 1963, 1968, 1970, 1971, 1972, 1973, 1974, 1978, 1998
Gymnastics (1): 1962
Swimming (9): 1960, 1963, 1964, 1965, 1966, 1974, 1975, 1976, 1977
Tennis (16): 1946, 1951, 1955, 1958, 1962, 1963, 1964, 1966, 1967, 1968, 1969, 1976 (tie with UCLA), 1991, 1993, 1994, 2002
Track & Field (28): 1926, 1930, 1931, 1935, 1936, 1937, 1938, 1939, 1940, 1941, 1942, 1943, 1949, 1950, 1951, 1952, 1953, 1954, 1955, 1958, 1961, 1963, 1965 (tie with Oregon), 1967i, 1967, 1968, 1972i, 1976 (i = indoor)
Volleyball (4): 1977, 1980, 1988, 1990
Water Polo (3): 1998, 2003, 2005
Women (13) Basketball (2): 1983, 1984
Golf (2): 2003, 2008
Soccer (1): 2007
Swimming (1): 1997
Tennis (2): 1983, 1985
Track & Field (1): 2001
Volleyball (3): 1981, 2002, 2003
Water Polo (1): 2004
Other championships (23) Men (14) Football (12): 1928 (Dickinson), 1931 (Helms), 1932 (Helms), 1939 (Dickinson), 1962 (AP), 1967 (AP), 1972 (AP), 1974 (UPI), 1976 (Billingsley), 1978 (UPI), 2003 (AP), 2004 (BCS)
Volleyball (2): 1949, 1950 (USVBA)
Women (9) Tennis (5): 1977 (AIAW); 1977, 1978 (USTA); 1979, 1980 (AIAW)
Volleyball (3): 1976, 1977, 1980 (AIAW)
Water Polo (1): 1999
Total: 109 championships
Other schools of note (very, very long) Here's the top 10 in terms of NCAA titles:
1. UCLA 103
2. Stanford 95
3. USC 86
4. Oklahoma State 48
T5. Arkansas 41
T5. LSU 41
7. Texas 39
8. Penn State 34
9. North Carolina 33
10. Michigan 32
And here's the breakdown for other schools of note:
Oklahoma State's national championships: 48 NCAA Titles Men (48) Baseball (1): 1959
Basketball (2): 1945, 1946
Cross Country (1): 1954
Golf (10): 1963, 1976, 1978, 1980, 1983, 1987, 1991, 1995, 2000, 2006
Wrestling (34): 1928, 1929, 1930, 1931, 1933, 1934, 1935, 1937, 1938, 1939, 1940, 1941, 1942, 1946, 1948, 1949, 1954, 1955, 1956, 1958, 1959, 1961, 1962, 1964, 1966, 1968, 1971, 1989, 1990, 1994, 2003, 2004, 2005, 2006
Other Championships (1) Women (1) Equestrian (1): 2000
Total: 49 championships
Arkansas' national championships: 41 NCAA Titles Men (41) Basketball (1): 1994
Cross Country (11): 1984, 1986, 1987, 1990, 1991, 1992, 1993, 1995, 1998, 1999, 2000
Indoor Track & Field (19): 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1997, 1998, 1999, 2000, 2003, 2005, 2006
Outdoor Track & Field (10): 1985, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2003, 2004 , 2005
Total: 41 championships
LSU's national championships: 41 NCAA Titles Men (16) Baseball (5): 1991, 1993, 1996, 1997, 2000
Boxing (1): 1949
Golf (4): 1940, 1942, 1947, 1955
Indoor Track & Field (2): 2001, 2004
Outdoor Track & Field (4): 1933, 1989, 1990, 2002
Women (25) Indoor Track & Field (11): 1987, 1989, 1991, 1993, 1994, 1995, 1996, 1997, 2002, 2003, 2004
Outdoor Track & Field (14): 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 2000, 2003, 2008
Other championships (2) Men (2) Football (2): 1958 (AP), 2003 (BCS)
Total: 43 championships
Texas' national championships: 39 NCAA Titles Men (17) Baseball (6): 1949, 1950, 1975, 1983, 2002, 2005
Golf (2): 1971, 1972
Swimming (9): 1981, 1988, 1989, 1990, 1991, 1996, 2000, 2001, 2002
Women (22) Basketball (1): 1986
Cross Country (1): 1986
Swimming (7): 1984, 1985, 1986, 1987, 1988, 1990, 1991
Tennis (2): 1993, 1995
Indoor Track & Field (6): 1986, 1988, 1990, 1998, 1999, 2006
Outdoor Track & Field (4): 1986, 1998, 1999, 2005
Volleyball (1): 1988
Other championships (8) Men (4) Football (4): 1963 (AP), 1969 (AP), 1970 (UPI), 2005 (BCS)
Women (4) Swimming (2): 1981, 1982
Outdoor Track & Field (1): 1982
Volleyball (1): 1981
Total: 47 championships
Penn State's national championships: 34 NCAA Titles Men (19) Boxing (1): 1932
Cross Country (3): 1942 (tie with Indiana), 1947, 1950
Gymnastics (12): 1948, 1953, 1954, 1957, 1959, 1960, 1961, 1965, 1976, 2000, 2004, 2007
Volleyball (2): 1994, 2008
Wrestling (1): 1953
Women (5) Fencing (1): 1983
Lacrosse (2): 1987, 1989
Volleyball (2): 1999, 2007
Co-ed (10) Fencing (10): 1990, 1991, 1995, 1996, 1997, 1998, 1999, 2000, 2002, 2007
Other championships (28) Men (18) Boxing (4): 1924, 1927, 1929, 1930
Football (2): 1982 (AP), 1986 (AP)
Soccer (11): 1926 (co-champs), 1929, 1933, 1936 (co), 1937 (co), 1938, 1939 (co), 1940 (co), 1949 (co), 1954, 1955 (co)
Wrestling (1): 1921
Women (10) Bowling (1): 1979
Fencing (2): 1980, 1981
Field Hockey (2): 1980, 1981
Gymnastics (2): 1978, 1980
Lacrosse (3): 1978, 1979, 1980
Total: 62 championships
North Carolina's national championships: 33 NCAA Titles Men (9) Basketball (4): 1957, 1982, 1993, 2005
Lacrosse (4): 1981, 1982, 1986, 1991
Soccer (1): 2001
Women (24) Basketball (1): 1994
Field Hockey (5): 1989, 1995, 1996, 1997, 2007
Soccer (18): 1982, 1983, 1984, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1996, 1997, 1999, 2000, 2003, 2006
Other championships (2) Men (1) Basketball (1): 1924 (Helms Athletic Foundation)
Women (1) Soccer (1): 1981 (AIAW)
Total: 35 championships
Michigan's national championships: 32 NCAA Titles Men (30) Baseball (2): 1953, 1962
Basketball (1): 1989
Golf (2): 1934, 1935
Gymnastics (3): 1963, 1970, 1999
Hockey (9): 1948, 1951, 1952, 1953, 1955, 1956, 1964, 1996, 1998
Swimming (11): 1937, 1938, 1939, 1940, 1941, 1948, 1957, 1958, 1959, 1961, 1995
Tennis (1): 1957
Outdoor Track & Field (1): 1923
Women (2) Field hockey (1): 2001
Softball (1): 2005
Other championships (21) Men (21) Football (12): 1901 (H), 1902 (H), 1903 (B), 1904 (B), 1910 (B), 1918 (B), 1923 (B), 1932 (D), 1933 (H), 1947 (B), 1948 (AP), 1997 (AP)
(H = Helms Athletic Foundation; B = Billingsley Report; D = Dickinson System)
Swimming (7): 1927, 1928, 1931, 1932, 1934, 1935, 1936
Trampoline (2): 1969, 1970 (I'm not kidding here.)
Total: 53 championships
Now, we hear so much about Duke's dominance in basketball. But a glance at the rest of their athletic program shows... well... not much.
Duke's national championships: 9 NCAA Titles Men (4) Basketball (3): 1991, 1992, 2001
Soccer (1): 1986
Women (5) Golf (5): 1999, 2002, 2005, 2006, 2007
Total: 9 championships
And here's the other Pac-10 schools and their NCAA titles:
Arizona: 17 NCAA Titles Men (6) Baseball (3): 1976, 1980, 1986
Basketball (1): 1997
Golf (1): 1992
Swimming (1): 2008
Women (11) Golf (2): 1996, 2000
Softball (8): 1991, 1993, 1994, 1996, 1997, 2001, 2006, 2007
Swimming (1): 2008
Other Championships (3) Women (3) Synchronized Swimming (3): 1980 (tie), 1981, 1984
Total: 20 championships
Arizona State: 21 NCAA Titles Men (11) Baseball (5): 1965, 1967, 1969, 1977, 1981
Golf (2): 1990, 1996
Gymnastics (1): 1986
Track & Field (2): 1977, 2008i (i = indoor)
Wrestling (1): 1988
Women (10) Golf (6): 1990, 1993, 1994, 1995, 1997, 1998
Softball (1): 2008
Track & Field (3): 2007i, 2007, 2008i (i = indoor)
Other Championships (115) Men (28) Archery (15): 1969, 1974, 1980, 1981, 1982, 1983, 1984, 1985, 1987, 1988, 1989, 1990, 1991, 1992, 1993
Badminton (13): 1978, 1980, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993
Women (57) Archery (21): 1969, 1970, 1971, 1972, 1976, 1977, 1978, 1979, 1980, 1981, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993
Badminton (17): 1971, 1975, 1976, 1978, 1979, 1980, 1981, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993
Golf (7): 1959, 1960, 1961, 1962, 1963, 1964, 1975 (AIAW)
Softball (2): 1972, 1973
Swimming (7): 1967, 1968, 1970, 1973, 1974, 1977, 1978 (AIAW)
Tennis (3): 1971, 1972, 1974
Co-ed (30) Archery (20): 1969, 1971, 1974, 1976, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993
Badminton (10): 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993
Total: 136 championships
California: 27 NCAA Titles Men (24) Baseball (2): 1947, 1957
Basketball (1): 1959
Golf (1): 2004
Gymnastics (4): 1968, 1975, 1997, 1998
Swimming (2): 1979, 1980
Track & Field (1): 1922
Water Polo (13): 1973, 1974, 1975, 1977, 1983, 1984, 1987, 1988, 1990, 1991, 1992, 2006, 2007
Women (3) Crew (2): 2005, 2006
Softball (1): 2002
Other Championships (38) Men (37) Crew (14): 1928, 1932, 1934, 1935, 1939, 1949, 1960, 1961, 1964, 1976, 1999, 2000, 2001, 2002
Football (2): 1920 (Helms Athletic Foundation), 1937 (Helms)
Rugby (21): 1980, 1981, 1982, 1983, 1985, 1986, 1988, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2004, 2005
Women (1) Crew (1): 1980 (AIAW)
(Note: From here on out, the "Other" category may be incomplete. These schools' websites don't bother to list all their national championships. Boo.)
Total: 65 championships
Oregon: 14 NCAA Titles Men (11) Basketball (1): 1939
Cross Country (5): 1971, 1973, 1974, 1977, 2007
Track & Field (5): 1962, 1964, 1965 (tie with USC), 1970 (tie with BYU & Kansas), 1984
Women (3) Cross Country (2): 1983, 1987
Track & Field (1): 1985
Total: 14 championships
Oregon State: 3 NCAA Titles Men (3) Baseball (2): 2006, 2007
Cross Country (1): 1961
Total: 3 championships
Washington: 4 NCAA Titles Women (4) Crew (3): 1997, 1998, 2001
Volleyball (1): 2005
Other Championships (20) Men (13) Crew (11): 1923, 1924, 1926, 1936, 1937, 1940, 1941, 1948, 1950, 1970, 1997
Football (2): 1960 (Helms), 1991 (UPI)
Women (7) Crew (7): 1981, 1982, 1983, 1984, 1985, 1987, 1988
Total: 24 championships
Washington State: 2 NCAA Titles Men (2) Boxing (1): 1937
Indoor Track & Field (1): 1977
Total: 2 championships
Hope that list helps.
So what does this all mean? In terms of NCAA titles, really, nobody else can come close to UCLA, Stanford, and USC.
But in terms of overall national championships, surprisingly enough, Arizona State leads the nation. (If anyone can find a school with more than 135 championships, please, let me know, and provide the pertinent info.) Of course, most of them came in badminton and archery, but then, we also have one in badminton, so it must be counted. Also, this is why I prefer to count by NCAA titles, not overall titles. Otherwise Arizona State would be considered the top athletic program in the nation, when they only have 21 NCAA titles. That's just for having dominant teams in basically two sports (archery & badminton). The sports, BTW, were dropped from varsity status at ASU in 1993.
As for football titles, I only list the major ones. I discounted the National Championship Foundation, among others, because it went back and selected MULTIPLE champions per year.

Yeah, that's not gonna cut it in my book.
For other schools you might want to know about, go to this site for the breakdown in what sports that school has won NCAA titles in. But careful, there are a few mistakes. For instance, if you click on Georgia, it has them with 24 NCAA titles (through Spring 2007), with two coming from women's golf. This is wrong. They only have one NCAA title in women's golf (from 2001) and only had 23 NCAA titles as of Spring 2007. They also gave Arizona an extra women's golf title. Whoever compiled the women's golf numbers for them should be fired posthaste.
But if you're wondering how I got the actual years, well, that's called research
