I spent a little time researching this but can't find any source for historic enrollment numbers at all of these schools.
I found articles referring to Billy Packer's Wake Forest team (1962) and that could be true, although current enrollment at Wake is 4400 (undergrad). Jacksonville claims to be the smallest school to play in the championship game (1970) and their current enrollment (3400) would make them smaller than Wake now, but then? Another article (on Xavier, currently 4000 undergrads) suggested it would be the smallest "since 1979", a year in which Indiana State's Larry Bird team was the smallest (current ISU undergrad enrollment is 8000+). The other participants that year were Michigan State, DePaul (over 20,000) and Penn (notable less for its size than it's no-scholarship Ivy Leageu credentials), so I'm not sure why they chose that reference.
I haven't been able to prove, therefore, that St. Bonaventure was not the smallest when it made the final four in 1970 (on Bob Lanier's big shoes and soft touch, but sadly with him on crutches). Current undergrad enrollment (2400) is, I think, only slightly higher than it was in 1970 (when they beat Davidson in the first round). I will, nevertheless, root for Davidson to establish the new mark this year.
Providence College played in two final fours and they are under 4,000 in enrollment. I believe Holy Cross also played in one back in the day and they are small as well.
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Holy Cross had under 1500 students when they won the 1947 title and 6 years later stunned the sports world by winning the College World Series in Omaha by outscoring W Michigan, Penn St, Texas and Missouri 52-17 in an 8 team double elimination format.
Penn in 1979.
1975 - The Indiana Hoosiers lost in the Mideast region's final to the Kentucky Wildcats.
Agnes Green
This year's (2008) Men's NCAA college basketball Final Four is being held at: San Antonio, Texas.
In 1975 Indiana finished the regular season 29-0, but lost to Kentucky in the Mideast Regional final.