| 'Til I Get It Right | John Doe and The Sadies | | | 3:19 | |
| [unknown] | John Doe | | | 1:09 | |
| 7 Holes | John Doe | | | 3:12 | |
| 7 Holes | John Doe | | | 3:11 | |
| A Beautiful Mind | John Doe (1200 Hobos) | | | 4:00 | |
| A Case of You | John Doe | | | 3:52 | |
| A Fool Such as I | John Doe and The Sadies | | | 2:32 | |
| A Little Help | John Doe | | | 3:39 | |
| A Little More Time | John Doe | | | 3:49 | |
| A Matter of Degrees (LP) | John Doe | | | ?:?? | |
| A Step Outside | John Doe | | | 3:58 | |
| After the Fall | John Doe | | | 3:06 | |
| All Along the Watchtower | Calexico, The Roots, Dan Hicks and The Hot Licks, Lee Ranaldo, J Mascis, John Doe,, Joe Henry, Mason Jennings, Al Kooper & Yo La Tengo | | | ?:?? | |
| Alone In Arizona | John Doe | | | 3:53 | |
| Always | John Doe | | | 4:55 | |
| Analyze This | John Doe (1200 Hobos) | | | 12:45 | |
| Are the Good Times Really Over for Good | John Doe and The Sadies | | | 2:38 | |
| Baby Doe | Jill Sobule & John Doe | | | 4:22 | |
| Baby Touch Me | John Doe | | | 3:29 | |
| Back to the Future | John Doe (1200 Hobos) | | | 7:06 | |
| Backroom | John Doe | | | 3:53 | |
| Ballad of a Thin Man | John Doe & The Million Dollar Bashers | | | ?:?? | |
| Beat-Up World | John Doe | | | 3:18 | |
| Because I Do | John Doe and Exene Cervenka | | | ?:?? | |
| Beer, Gas, Ride Forever | John Doe | | | 3:28 | |
| Before I Wake | John Doe and The Sadies | | | 2:32 | |
| Better Just | John Doe | | | ?:?? | |
| Beyond You | John Doe and Exene Cervenka | | | ?:?? | |
| Big Moon | John Doe | | | 3:25 | |
| Blue Moon | Bud Shank, Buddy Collette, John Doe, Red Mitchell, Mel Lewis | | | 2:45 | |
| Buckets of Rain (Dec 27, 1995, KCRW Studio, Santa Monica, CA) | John Doe with Jennifer Jason Leigh | | | ?:?? | |
| By the Light | John Doe | | | 2:53 | |
| By the Light | John Doe | | | 2:36 | |
| Call of the Wreckin' Ball | John Doe with Jim and Jennie and The Pinetops | | | 3:39 | |
| Catch Me | John Doe | | | 3:17 | |
| Charges | Papoose feat. John Doe | | | ?:?? | |
| Closet of Dreams | John Doe | | | 3:45 | |
| Commercial | John Doe (1200 Hobos) | | | 0:41 | |
| Cottage in the ’Dale | John Doe | | | 3:04 | |
| D3 | John Doe | | | 6:55 | |
| Darling Underdog | John Doe | | | 2:52 | |
| Darling Underdog | Jill Sobule & John Doe | | | 2:46 | |
| Darling Underdog | John Doe | | | 2:45 | |
| Destroying Angels | Garbage with John Doe & Exene Cervenka | | 2.5 | 5:01 | |
| Destroying Angels | John Doe | | | 3:22 | |
| Detroit City | John Doe and The Sadies | | | 2:55 | |
| Domestic Disturbance | John Doe (1200 Hobos) | | | 0:39 | |
| Don't Forget | John Doe | | | 3:40 | |
| Don’t Forget How Much I Love You | John Doe | | | 3:40 | |
| Down South | John Doe | | | 2:57 | |
| Drink of Water | John Doe | | | 3:42 | |
| Dyin' to Get Home | John Doe | | | 3:44 | |
| Dying to Get Home | John Doe | | | 3:03 | |
| El Romance-0 | John Doe | | | 3:21 | |
| Elevated Mind Trips | John Doe | | | 5:24 | |
| Employee of the Month | John Doe | | | 4:00 | |
| Employee of the Month | Jill Sobule & John Doe | | | 3:34 | |
| Far Away (From the North Country) | John Doe | | | 2:43 | |
| Faraway (From the North County) | John Doe | | | 2:43 | |
| Forever for You | John Doe | | | 4:19 | |
| Forever for You | John Doe | | | 4:21 | |
| Forever Young | John Doe & Lucy Schwartz | | | 4:26 | |
| Freestyle | John Doe | | | 1:54 | |
| Frequency (Raul Rincon remix) (feat. Gray) | John Doe | | | 4:03 | |
| Get On Board | John Doe | | | 2:35 | |
| Giant Step Backward | John Doe | | | 4:44 | |
| Go Baby Go | John Doe | | | 3:26 | |
| Golden State | John Doe | | | 3:08 | |
| Grain of Salt | John Doe | | | 4:29 | |
| Grain of Salt | John Doe | | | 4:31 | |
| Guilty Bystander | John Doe | | | 3:00 | |
| Handsome Devil | John Doe | | | 2:40 | |
| Heartless | John Doe | | | 2:29 | |
| Hearts | John Doe | | | 0:16 | |
| Help Me Make It Through the Night | John Doe and The Sadies | | | 3:36 | |
| hidden track | John Doe (1200 Hobos) | | | 1:25 | |
| Higher Learning | John Doe (1200 Hobos) | | | 6:13 | |
| Highway 5 | John Doe & Neko Case | | | 2:52 | |
| Highway 61 Revisited (Oct 6, 2007, Hardly Strictly Bluegrass Festival, San Francisco, CA) | Los Lobos with Dave Alvin and John Doe | | | ?:?? | |
| Hot Burrito No. 2 | John Doe | | | ?:?? | |
| Hotel Ghost | John Doe | | | 2:27 | |
| Husbands and Wives | John Doe and The Sadies | | | 2:42 | |
| Hwy 5 | John Doe | | 3 | 2:53 | |
| Hwy 5 | John Doe | | | 2:52 | |
| I Can't Hold Myself in Love | John Doe | | | 3:12 | |
| I Dreamed I Saw St. Augustine | John Doe | | | 3:15 | |
| I Dreamed I Saw St. Augustine (Mar 04, 1989, McCabe's Guitar Shop, Santa Monica, CA) | John Doe | | | ?:?? | |
| I Kissed a Girl | Jill Sobule & John Doe | | | 3:20 | |
| I May Be Wrong | Bud Shank, Buddy Collette, John Doe, Red Mitchell, Mel Lewis | | | 5:07 | |
| I Shall Be Released (Sep 19, 2002, Cat's Cradle Carrboro, NC) | John Doe, Kristin Hersh, & Grant‐Lee Phillips | | | ?:?? | |
| I Still Miss Someone | John Doe and The Sadies | | | 2:19 | |
| I'll Be Your Baby Tonight (Feb 28, 1987, McCabe's Guitar Shop, Santa Monica, CA) | John Doe and Harry Dean Stanton & Harry Dean Stanton | | | ?:?? | |
| I’m in Love With a Girl | Jill Sobule & John Doe | | | 2:26 | |
| If I Should Die | John Doe feat. Nature | | | 3:15 | |
| Imitation of the Blues (acoustic) | John Doe | | | ?:?? | |
| It Just Dawned on Me | John Doe and Exene Cervenka | | | ?:?? | |
| It Just Dawned On Me | John Doe and The Sadies | | | 2:34 | |
| It's Only Love | John Doe | | | 3:21 | |
| Jump Into My Arms | John Doe | | | 2:32 | |
| Just for the Hell of It | John Doe | | | 2:47 | |
