St. Andrews College in North Carolina, is the home of the Thistle and Shamrock radio program archives. Don't know whether they feature folk music per se, but I believe they feature Scottish music and when I visited there with my son, they featured bagpipe lessons.

The University of Kentucky seems to have a very lively interest in promoting Appalachian folk music. They are affiliated with June Appal recordings. Also, here are the colleges that contribute to the Digital Library of Appalachia, they are also a good bet:

    Berea College : Hutchins Library
    Cumberland College : Hagan Memorial Library
    Lees-McRae College : James H. Carson Library
    Lincoln Memorial University : Carnegie Vincent Library and Lincoln Library
    Tennessee Wesleyan College : Merner Pfeiffer Library
    Warren Wilson College : Pew Learning Center and Ellison Library
    West Virginia Wesleyan College : Annie Merner Pfeiffer Library

Check with the various UNC campuses as well.

Good luck!