Those two, afaik.
The "Omaha College Baseball Hall of Fame" is really the "Omaha College World Series Hall of Fame" but uses Omaha in the title due to copyright restrictions (MLB owns and licenses the copyright to "College World Series" to the NCAA). It was started 2013 by the same Chicago-based company that created and promotes the College Home Run Derby as a way to bring attention to the then three year-old event.
The "National College Baseball Hall of Fame" (NCHoF) is run by the Lubbock-based College Baseball Foundation. The non-profit organization was established in 2004 and inducted their inaugural HoF class in 2006. The NCHoF Museum was planned to open on land to be donated by the City of Lubbock, but fell through due to missing a ground-breaking deadline. It also bestows annual awards to players and coaches: Skip Bertman National Coach of the Year, National Pitcher of the Year Award, John Olerud Two-Way Player of the Year Award, and the Brooks Wallace (Shortstop of the Year) Award.