Maryland - mens soccer '05, womens bball '06, women's field hockey '05+'06 (i forget if field hockey is spring or fall, but they won both years anyways)
UNC - mens bball '09, womens soccer '08, women's field hockey '09
stanford - they do it just about every year because of the non-revenue sports (
http://champions.stanford.edu/history/stanfords-national-championships/)
my brother went to maryland and they did it the year after he graduated, and unc did it just before I moved into chapel hill so i had to hear about it way too often...
you can just punch in 'whatever school' national championships and then look on wikipedia to see all of them for a given school