Here's my lift of top 10 programs based upon unbiased information. I simply used the amount of National Championships won since 1900:
#1 Notre Dame Fighting Irish - Though their last National Championship was more than twenty years ago, the Fighting Irish are still on top of the heap when it comes to the total amount of titles they've won. Their thirteen titles place them three ahead of the second place college and well ahead of the schools behind that. From the 1910's through the 1980's, the Notre Dame Fighting Irish were able to win at least one National Championship in every decade except the 1950's. In fact, in the 1940's alone they won the National Title on four different occasions.
#2 Alabama Crimson Tide - With ten National Championships to their credit, the University of Alabama is one of only two colleges with double digit National Titles to their name. Most of their titles were won under the watch of their famous head coach Paul "Bear" Bryant.
#3 (Tie) USC Trojans - The University of Southern California has won nine National Championships, the first in 1931 and the last in 2004. The Trojans won three titles during the 1970's and then back-to-back titles in 2003 and 2004.
#3 (Tie) Michigan Wolverines - The Michigan Wolverines are one of the most storied football programs in all of college football. The Wolverines got off to a great start in the last century by winning the National Title in 1901, 1902, 1903, and 1904. Michigan won it's eighth title in 1948 and didn't follow it up with another one until almost fifty years later when they won their ninth in 1997.
#4 (Tie) Ohio State Buckeyes - The Ohio State Buckeyes have proven themselves year in and year out as one of the class teams in the Big 10. With seven National Championships won by the Buckeyes, Ohio State has seen it's fair share of success.
#4 (Tie) Oklahoma Sooners - One of the more dominant teams of the 1950's and then again the 1970's, the Oklahoma Sooners are one of the all-time great football programs in college football. With the exception of their last two National Titles that came in 1985 and 2000, the Sooners have seemed to win their championships in bunches. They won three titles in the 1950's (1950, 1955, and 1956) and then won back-to-back titles in 1974 and 1975.
#5 Minnesota Golden Gophers - The Minnesota Golden Gophers are the team in this list that usually surprises most casual college football fans. Minnesota has won six National Championships, though none since 1960. In fact, the Golden Gophers have one of the more impressive dynasty claims in that they won five National Titles in eight years from 1934 to 1941 (1934, 1935, 1936, 1940, and 1941).
#6 (Tie) Miami Hurricanes - The Hurricanes' inclusion on this list is really quite amazing as they did not win their first National Championship until 1983. In the next eighteen years they would add four more titles to achieve their current state of owning five National Championships.
#6 (Tie) Nebraska Cornhuskers - Similar to the University of Miami, the University of Nebraska had a late start when it came to accumulating their National Championships. They won their first one in 1970 as part of their back-to-back titles of 1970 and 1971. They then added three titles in four years when they won the National Championship in 1994, 1995, and 1997.
#6 (Tie) Pittsburgh Panthers - The University of Pittsburgh is another team that many would not expect to find on this list though they are the proud owners of five National Championships as well. The team earned their first four titles between 1910 and 1937 and didn't add the fifth one until 1976.