| (Don't Fear) The Reaper [Blue Öyster Cult] | Cover | 16 |
| (Was I) In Your Dreams | Being There | 82 |
| (What's So Funny 'Bout) Peace, Love and Understanding [Nick Lowe] | Cover | 2 |
| ...And Then You Cut It in Half | Warmer | 3 |
| 36 Inches High [Jim Ford] | Cover | 7 |
| A Beard Of Stars [T. Rex] | Cover | 2 |
| A Bowl and a Pudding | Cousin | 2 |
| A Fool Such As I [Trader (Elvis Presley)] | Cover | 2 |
| A Lifetime to Find | Cruel Country | 55 |
| A Long Time Ago | | 4 |
| A Magazine Called Sunset | More Like The Moon EP | 86 |
| A Robin or a Wren | Love Is the King | 11 |
| A Shot In The Arm | Summerteeth | 1097 |
| Acuff-Rose | Anodyne | 115 |
| Ain't It a Shame | Twilight Override | 7 |
| Ain't Much To Say | | 1 |
| Airline To Heaven | Mermaid Avenue, Vol. 2 | 243 |
| All Across the World | Cruel Country | 24 |
| All The Same To Me | Weird Tales | 7 |
| All The Young Dudes [David Bowie/Mott The Hoople] | Cover | 2 |
| Alone | | 7 |
| Amar Bharati | Twilight Override | 4 |
| Amarillo Highway [Terry Allen] | Cover | 1 |
| Ambulance | Cruel Country | 8 |
| An Empty Corner | Ode to Joy | 15 |
| Anarchy In The UK [Sex Pistols] | Cover | 1 |
| And Your Bird Can Sing [The Beatles] | Cover | 2 |
| Androgynous [The Replacements] | Cover | 1 |
| Annihilation | Hot Sun Cool Shroud | 76 |
| Another Man's Done Gone [Woody Guthrie] | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 30 |
| Answers | | 2 |
| Any Major Dude Will Tell You [Donald Fagen/Walter Becker (Steely Dan)] | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 1 |
| Art of Almost | The Whole Love | 380 |
| Ashes Of American Flags | Yankee Hotel Foxtrot | 312 |
| At Least That's What You Said | A Ghost Is Born | 492 |
| At My Window Sad And Lonely | Mermaid Avenue | 30 |
| Auld Lang Syne | | 1 |
| Baba O'Riley [The Who] | Cover | 1 |
| Bad Day Lately | Love Is the King | 2 |
| Bang Bang (My Baby Shot Me Down) [Cher] | Cover | 1 |
| Barstool Blues | | 1 |
| Be Not So Fearful [Bill Fay] | Cover | 60 |
| Before Us | Ode to Joy | 60 |
| Betrayed | Twilight Override | 11 |
| Better Song | Twilight Override | 1 |
| Bird Without a Tail/Base of My Skull | Cruel Country | 185 |
| Black Eye | March 16-20, 1992 | 48 |
| Black Moon | The Whole Love | 46 |
| Blasting Fonda | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 23 |
| Blood Of The Lamb | Mermaid Avenue, Vol. 2 | 34 |
| Blue Eyed Soul | A.M. | 16 |
| Bob Dylan's 49th Beard | More Like The Moon EP | 121 |
| Boeing Spacearium | | 1 |
| Bombs Above | Warm | 26 |
| Born Alone | The Whole Love | 264 |
| Box Full Of Letters | A.M. | 619 |
| Bright Leaves | Ode to Joy | 67 |
| Bright Phoebus [Lal and Mike Waterson] | Cover | 2 |
| Broken Arrow [Buffalo Springfield] | Cover | 11 |
| Bull Black Nova | Wilco (the album) | 296 |
| Cajun Angel | | 1 |
| California Stars | Mermaid Avenue | 1013 |
| Camera | More Like The Moon EP | 60 |
| Can't Stand It | Summerteeth | 168 |
| Can't Stand Yourself | Arabella | 3 |
| Can't Stop Talking | | 2 |
| Candyfloss | Summerteeth | 104 |
| Capitol City | The Whole Love | 52 |
| Cars Can't Escape | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 62 |
| Casino Queen | A.M. | 372 |
| Caught Up in the Past | Twilight Override | 14 |
| Chelsea Walls Theme | Chelsea Walls | 2 |
| Chest Fever [The Band] | Cover | 1 |
| Childlike and Evergreen | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 7 |
| Chinese Apple | Loose Fur | 15 |
| Christ For President | Mermaid Avenue | 144 |
| Cinnamon Girl [Neil Young] | Cover | 11 |
| Citizens | Ode to Joy | 1 |
| Climbing [Meat Puppets] | Cover | 1 |
| Cock In My Pocket [Iggy Pop (The Stooges)] | Cover | 3 |
| Cold Hard World [Daniel Johnston] | Cover | 1 |
| Cold Shoulder | Still Feel Gone | 1 |
| Cold Slope | Star Wars | 81 |
| Cold Turkey | | 2 |
| Colon Song | | 1 |
| Color Me Impressed [The Replacements] | Cover | 8 |
| Come Together [The Beatles] | Cover | 2 |
| Comment (If All Men Are Truly Brothers) [Charles Wright and the Watts 103rd St. Rhythm Band] | Cover | 10 |
| Common Sense | Schmilco | 1 |
| Company In My Back | A Ghost Is Born | 293 |
| Cortez the Killer [Neil Young] | Cover | 1 |
| Cosmic Dancer [T. Rex] | Cover | 2 |
| Country Disappeared | Wilco (the album) | 29 |
| Country Song Upside-Down | Cruel Country | 18 |
| Cousin | Cousin | 37 |
| Cruel Country | Cruel Country | 189 |
| Cruel To Be Kind [Nick Lowe] | Cover | 9 |
| Cry All Day | Schmilco | 81 |
| Cry Baby Cry | Twilight Override | 11 |
| Cut Your Hair [Pavement] | Cover | 2 |