2004 The Best of John Fahey, Vol. 2: 1964–1983 (Takoma)
Of Rivers and Religion/After the Ball (Warner Bros.)
2005 On the Sunny Side of the Ocean (Brook Records)
2006 Sea Changes & Coelacanths: A Young Person's Guide to John Fahey (Table of the Elements)
2006 Vanguard Visionaries (Vanguard)
2009 Twilight on Prince Georges Avenue: Essential Recordings (Rounder)
2011 Your Past Comes Back To Haunt You: The Fonotone Years 1958–1965 (Dust-to-Digital)
Tribute albums:
1979 A Tribute to John Fahey (Kicking Mule)
2006 I Am the Resurrection: A Tribute to John Fahey (Vanguard)
Friends of Fahey Tribute (Slackertone)
The Revenge of Blind Joe Death: The John Fahey Tribute Album (Takoma)
2007 The Great Koonaklaster Speaks: A John Fahey Celebration (Table of the Elements)