| If That's Alright | Still Feel Gone | 21 |
| Immigrant Song | Cover | 27 |
| Impossible Germany | Sky Blue Sky | 417 |
| In A Future Age | Summerteeth | 44 |
| In The Street | Cover | 8 |
| Interview | | 22 |
| Intro | | 5 |
| It's Just That Simple | A.M. | 59 |
| James Alley Blues | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 30 |
| Jesus, Etc. | Yankee Hotel Foxtrot | 671 |
| John Wesley Harding | Cover | 14 |
| Jumping Jack Flash | Cover | 1 |
| Just A Kid | The SpongeBob SquarePants Movie | 14 |
| Just Wanted to Thank You | | 2 |
| Kamera | Yankee Hotel Foxtrot | 215 |
| Kicking Television | A Ghost Is Born | 55 |
| Kingpin | Being There | 332 |
| Laminated Cat | Loose Fur | 66 |
| Leave Me (Like You Found Me) | Sky Blue Sky | 1 |
| Less Than You Think | A Ghost Is Born | 62 |
| Let's Hear It For Rock and Roll | | 18 |
| Let's Not Get Carried Away | Sky Blue Sky Tour EP | 16 |
| Lies of the Living Dead | | 3 |
| Listen To Her Heart | Cover | 21 |
| Livin' After Midnight | Cover | 1 |
| Lost Love | Weird Tales | 21 |
| Love Will Keep Us Together | Cover | 2 |
| Misunderstood | Being There | 477 |
| Modern World | | 1 |
| Monday | Being There | 333 |
| More Like The Moon | More Like The Moon EP | 8 |
| Muzzle Of Bees | A Ghost Is Born | 260 |
| My Darling | Summerteeth | 45 |
| New Madrid | Anodyne | 275 |
| New Years Countdown | | 1 |
| No Church Tonight | | 1 |
| No Romance | | 1 |
| No Sense In Lovin' | Anodyne | 24 |
| Not For The Season | | 149 |
| Nothing'severgonnastandinmyway(again) | Summerteeth | 87 |
| Oklahoma USA | Cover | 6 |
| On And On And On | Sky Blue Sky | 41 |
| One By One | Mermaid Avenue | 120 |
| One Hundred Years From Now | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 2 |
| One Sunday Morning (Song For Jane Smiley's Boyfriend) | The Whole Love | 75 |
| One Wing | Wilco (the album) | 159 |
| Open Mind | The Whole Love | 11 |
| Outta Mind (Outta Sight) | Being There | 93 |
| Outtasite (Outta Mind) | Being There | 426 |
| Outtro | | 1 |
| Paranoid | Cover | 2 |
| Passenger Side | A.M. | 406 |
| Pecan Pie | Down By The Old Mainstream | 53 |
| Pick Up The Change | A.M. | 130 |
| Pieholden Suite | Summerteeth | 24 |
| Piss It Away | | 2 |
| Please Be Patient With Me | Sky Blue Sky | 13 |
| Political Science | Cover | 22 |
| Poor Places | Yankee Hotel Foxtrot | 329 |
| Pot Kettle Black | Yankee Hotel Foxtrot | 196 |
| Promising | Chelsea Walls | 9 |
| Psycho Killer | Cover | 1 |
| Radio Cure | Yankee Hotel Foxtrot | 139 |
| Rainbow Connection | Cover | 1 |
| Red-Eyed And Blue | Being There | 392 |
| Reincarnation | Cover | 20 |
| Remember The Mountain Bed | Mermaid Avenue, Vol. 2 | 154 |
| Reservations | Yankee Hotel Foxtrot | 198 |
| Rising Red Lung | The Whole Love | 21 |
| Rock n Roll Queen | | 1 |
| Sandusky | March 16-20, 1992 | 2 |
| Satan, Your Kingdom Must Come Down | March 16-20, 1992 | 23 |
| Say You Miss Me | Being There | 47 |
| Screen Door | No Depression | 23 |
| Secret Of The Sea | Mermaid Avenue, Vol. 2 | 21 |
| Shake It Off | Sky Blue Sky | 44 |
| She's A Jar | Summerteeth | 319 |
| Should I Stay Or Should I Go? | Cover | 1 |
| Should've Been In Love | A.M. | 74 |
| Shouldn't Be Ashamed | A.M. | 88 |
| Side With The Seeds | Sky Blue Sky | 165 |
| Sky Blue Sky | Sky Blue Sky | 71 |
| Smoke on the Water | Cover | 1 |
| Someday Some Morning Sometime | Mermaid Avenue, Vol. 2 | 30 |
| Someday Soon | Being There | 114 |
| Someone Else's Song | Being There | 139 |
| Something In The Air | Cover | 19 |
| Sonny Feeling | Wilco (the album) | 46 |
| Spiders (Kidsmoke) | A Ghost Is Born | 475 |
| Standing O | The Whole Love | 48 |
| Sugar Baby | Cover | 18 |
| Summer Teeth | Summerteeth | 110 |
| Sunday Bloody Sunday | Cover | 1 |
| Sunken Treasure | Being There | 325 |
| TV Eye | Cover | 2 |
| Thank You Friends | Cover | 16 |
| That's Not The Issue | A.M. | 116 |
| The Auld Triangle | Cover | 14 |
| The Good Part | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 12 |
| The Late Greats | A Ghost Is Born | 390 |