If you include women's BBall, Pat Summitt, the women's Basketball coach at Tennessee, won her 1,000th game. In the graphic in this article:
http://www.nytimes.com/2009/02/06/sports/ncaabasketball/06tennessee.html?ref=ncaabasketball
Bobby Knight had 902.
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1 Kentucky............... 2027
2 Kansas.................. 2009
3 North Carolina...... 2007
4 Duke..................... 1912
5 Syracuse.............. 1783
6 Temple.................. 1740
7 St. John's.............. 1703
8 UCLA..................... 1686
9 Notre Dame........... 1674
10 Pennsylvania....... 1664
the University of Kentucky has the NCAA record for most wins in College Basketball history