| Shush | In Times of Dragons | 63 |
| Fire to Your Plain | Abnormally Attracted to Sin | 57 |
| Big Wheel | American Doll Posse | 34 |
| Cornflake Girl | Under the Pink | 33 |
| Crucify | Little Earthquakes | 33 |
| Precious Things | Little Earthquakes | 32 |
| Iieee | From the Choirgirl Hotel | 25 |
| Pandora's Aquarium | From the Choirgirl Hotel | 23 |
| Bliss | To Venus and Back | 22 |
| A Sorta Fairytale | Scarlet's Walk | 21 |
| God | Under the Pink | 20 |
| Little Amsterdam | Boys for Pele | 20 |
| Mary | Little Earthquakes — B-sides | 20 |
| Bells For Her | Under the Pink | 19 |
| Black Dove (January) | From the Choirgirl Hotel | 19 |
| Witness | The Beekeeper | 19 |
| Putting the Damage On | Boys for Pele | 18 |
| Horses | Boys for Pele | 17 |
| In Times of Dragons | In Times of Dragons | 17 |
| Stronger Together | In Times of Dragons | 17 |
| Winter | Little Earthquakes | 17 |
| Body and Soul | American Doll Posse | 16 |
| Honey | Under the Pink — B-sides | 16 |
| Ruby Through the Looking Glass | Scarlet's Walk — B-sides | 16 |
| Pretty Good Year | Under the Pink | 15 |
| Sweet Sangria | Scarlet's Walk | 15 |
| Taxi Ride | Scarlet's Walk | 15 |
| Don't Make Me Come To Vegas | Scarlet's Walk | 14 |
| Spring Haze | To Venus and Back | 14 |
| Addition of Light Divided | Ocean to Ocean | 13 |
| Angelshark | In Times of Dragons | 13 |
| Code Red | American Doll Posse | 13 |
| Caught a Lite Sneeze | Boys for Pele | 12 |
| Crazy | Scarlet's Walk | 12 |
| Fast Horse | Abnormally Attracted to Sin | 12 |
| Gasoline Girls | In Times of Dragons | 12 |
| Girl | Little Earthquakes | 12 |
| Song of Sorrow | In Times of Dragons | 12 |
| Tombigbee | Scarlet's Walk — B-sides | 11 |
| Your Cloud | Scarlet's Walk | 11 |
| Little Earthquakes | Little Earthquakes | 10 |
| Mother Revolution | The Beekeeper | 10 |
| Give | Abnormally Attracted to Sin | 9 |
| Past the Mission | Under the Pink | 9 |
| Take to the Sky | Little Earthquakes — B-sides | 9 |
| Baker Baker | Under the Pink | 8 |
| Climb | Native Invader | 8 |
| Silent All These Years | Little Earthquakes | 8 |
| St. Teresa | In Times of Dragons | 8 |
| Icicle | Under the Pink | 7 |
| Virginia | Scarlet's Walk | 7 |
| Rattlesnakes | Strange Little Girls | 6 |
| Strange | Scarlet's Walk | 6 |
| China | Little Earthquakes | 5 |
| Cooling | From the Choirgirl Hotel — B-sides | 5 |
| Josephine | To Venus and Back | 5 |
| Sugar | Little Earthquakes — B-sides | 5 |
| Blue Lotus | In Times of Dragons | 4 |
| Lovesong | Cover | 4 |
| Ocean to Ocean | Ocean to Ocean | 4 |
| Smokey Joe | American Doll Posse | 4 |
| Upside Down | Little Earthquakes — B-sides | 4 |
| Waitress | Under the Pink | 4 |
| Famous Blue Raincoat | Cover | 3 |
| Martha's Foolish Ginger | The Beekeeper | 3 |
| Poison & Wine | Cover | 3 |
| Riot Poof | To Venus and Back | 3 |
| Bachelorette | From the Choirgirl Hotel — B-sides | 2 |
| Bouncing Off Clouds | American Doll Posse | 2 |
| Graveyard | Boys for Pele — B-sides | 2 |
| Merman | From the Choirgirl Hotel — B-sides | 2 |
| Over the Rainbow | Cover | 2 |
| Twinkle | Boys for Pele | 2 |
| Way Down | Boys for Pele | 2 |
| Yo George | American Doll Posse | 2 |
| 97 Bonnie and Clyde | Strange Little Girls | 1 |
| American Pie | Cover | 1 |
| Falling Slowly | Cover | 1 |
| The Lion Sleeps Tonight | Cover | 1 |
| Me And a Gun | Little Earthquakes | 1 |
| Not the Red Baron | Boys for Pele | 1 |
| Real Men | Strange Little Girls | 1 |
| Reindeer King | Native Invader | 1 |
| Sister Janet | Under the Pink — B-sides | 1 |
| Streets Of Philadelphia | Cover | 1 |