Courtesy of SBZipfan on BigSoccer.com:
Top 8 seeds were first listed in 1997. Since then, Connecticut 2000, UCSB 2006, Indiana 2012, and Virginia 2014 were champions not in the top 8.
http://fs.ncaa.org/Docs/stats/m_soccer_RB/2011/D1Brackets.pdf
https://en.wikipedia.org/wiki/NCAA_Division_I_Men's_Soccer_Championship
That is actually more than I would have guessed.