| (Don't Fear) The Reaper | Cover | 15 |
| (Was I) In Your Dreams | Being There | 77 |
| 36 Inches High | Cover | 7 |
| A Beard Of Stars | Cover | 2 |
| A Fool Such As I | Cover | 2 |
| A Long Time Ago | | 1 |
| A Magazine Called Sunset | More Like The Moon EP | 52 |
| A Shot In The Arm | Summerteeth | 831 |
| Acuff-Rose | Anodyne | 97 |
| Ain't Much To Say | | 1 |
| Airline To Heaven | Mermaid Avenue, Vol. 2 | 216 |
| All The Same To Me | Weird Tales | 7 |
| All The Young Dudes | Cover | 1 |
| Alone | | 5 |
| Anarchy In The UK | Cover | 1 |
| Another Man's Done Gone | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 28 |
| Answers | | 2 |
| Any Major Dude Will Tell You | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 1 |
| Art of Almost | The Whole Love | 138 |
| Ashes Of American Flags | Yankee Hotel Foxtrot | 247 |
| At Least That's What You Said | A Ghost Is Born | 330 |
| At My Window Sad And Lonely | Mermaid Avenue | 18 |
| Auld Lang Syne | | 1 |
| Baba O'Riley | Cover | 1 |
| Barstool Blues | | 1 |
| Be Not So Fearful | Cover | 46 |
| Black Eye | March 16-20, 1992 | 47 |
| Black Moon | The Whole Love | 43 |
| Blasting Fonda | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 20 |
| Blood Of The Lamb | Mermaid Avenue, Vol. 2 | 29 |
| Blue Eyed Soul | A.M. | 11 |
| Bob Dylan's 49th Beard | More Like The Moon EP | 109 |
| Boeing Spacearium | | 1 |
| Born Alone | The Whole Love | 143 |
| Box Full Of Letters | A.M. | 240 |
| Broken Arrow | Cover | 11 |
| Bull Black Nova | Wilco (the album) | 157 |
| Cajun Angel | | 1 |
| California Stars | Mermaid Avenue | 570 |
| Camera | More Like The Moon EP | 1 |
| Can't Stand It | Summerteeth | 151 |
| Can't Stand Yourself | Arabella | 3 |
| Can't Stop Talking | | 2 |
| Candyfloss | Summerteeth | 88 |
| Capitol City | The Whole Love | 49 |
| Cars Can't Escape | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 34 |
| Casino Queen | A.M. | 334 |
| Chelsea Walls Theme | Chelsea Walls | 2 |
| Childlike and Evergreen | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 5 |
| Chinese Apple | Loose Fur | 14 |
| Christ For President | Mermaid Avenue | 134 |
| Cock In My Pocket | Cover | 3 |
| Cold Shoulder | Still Feel Gone | 1 |
| Cold Turkey | | 2 |
| Colon Song | | 1 |
| Color Me Impressed | Cover | 7 |
| Come Together | Cover | 2 |
| Comment (If All Men Are Truly Brothers) | Cover | 10 |
| Company In My Back | A Ghost Is Born | 191 |
| Country Disappeared | Wilco (the album) | 15 |
| Cruel To Be Kind | Cover | 9 |
| Dad Says | | 1 |
| Daggers Drawn | Down With Wilco | 4 |
| Dash 7 | A.M. | 8 |
| Dawned On Me | The Whole Love | 144 |
| Days Of Wine And Booze | Down With Wilco | 7 |
| Dead Flowers | | 1 |
| Dear Employer (The Reason I Quit) | Down With Wilco | 8 |
| Deeper Down | Wilco (the album) | 54 |
| Dirty Old Town | Cover | 1 |
| Don't You Honey Me | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 22 |
| Down In The Willow Garden | | 7 |
| Dreamer In My Dreams | Being There | 50 |
| Dreaming | Cover | 4 |
| Drown | Cover | 1 |
| Dueling Banjos | | 5 |
| ELT | Summerteeth | 53 |
| Easter Bunny ditty | | 1 |
| Either Way | Sky Blue Sky | 42 |
| Elegant Transaction | Loose Fur | 2 |
| Ever Fallen In Love | Cover | 5 |
| Everlasting Everything | Wilco (the album) | 8 |
| Everybody Knows This Is Nowhere | | 2 |
| Fake Plastic Trees | Cover | 5 |
| Far, Far Away | Being There | 168 |
| Fatal Wound | March 16-20, 1992 | 1 |
| Feed Of Man | Mermaid Avenue, Vol. 2 | 31 |
| Forget The Flowers | Being There | 296 |
| Froggie Went A Courtin' | | 1 |
| Give Back The Key To My Heart | Anodyne | 39 |
| Goodnight Irene | Cover | 1 |
| Gun | Still Feel Gone | 84 |
| Gut Feeling / Slap Your Mammy | Cover | 1 |
| Handshake Drugs | A Ghost Is Born | 552 |
| Hank, Karen, and Elvis | | 1 |
| Happy Birthday | | 18 |
| Hate It Here | Sky Blue Sky | 265 |
| Heart Like a Wheel | | 3 |
| Heavy Metal Drummer | Yankee Hotel Foxtrot | 573 |
| Hell Is Chrome | A Ghost Is Born | 134 |