| Song title | Album | Released |
| "Ender Will Save Us All
| Summer's Kiss (EP) | 2002 |
| A Plain Morning
| The Swiss Army Romance | 2000 |
| A Year In The Past, Forever In The Future
| The Wire Tapes | 2007 |
| Again I Go Unnoticed
| The Places You Have Come to Fear the Most | 2001 |
| Again I Go Unnoticed
| The Swiss Army Romance | 2000 |
| Again I Go Unnoticed (Live)
| MTV Unplugged 2.0 | 2002 |
| Age Six Racer
| The Swiss Army Romance | 2000 |
| Am I Missing
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Angels of the Silences
| The Wire Tapes | 2007 |
| Anyone, Anyone?
| The Drowning (EP) | 2001 |
| As Lovers Go
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Bend and Not Break
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Better
| The Wire Tapes | 2007 |
| Carry This Picture
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Carve Your Heart Out Yourself
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Catch
| The Wire Tapes | 2007 |
| Clean Breaks
| The Shade of Poison Trees | 2007 |
| Crazy
| The Wire Tapes | 2007 |
| Currents
| Dusk And Summer | 2006 |
| Don't Wait
| Dusk And Summer | 2006 |
| Don't Wait (Live)
| AOL Sessions EP (iTunes Exclusive) | 2006 |
| Drowning
| The Drowning (EP) | 2001 |
| Dusk and Summer
| Dusk And Summer | 2006 |
| El Scorcho
| The Wire Tapes | 2007 |
| Ender Will Save Us All
| The Swiss Army Romance | 2000 |
| Fever Dreams
| The Shade of Poison Trees | 2007 |
| For Justin
| The Drowning (EP) | 2001 |
| For You to Notice
| So Impossible (EP) | 2001 |
| For You to Notice (Live)
| MTV Unplugged 2.0 | 2002 |
| Ghost of a Good Thing
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Hands Down
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Hands Down
| So Impossible (EP) | 2001 |
| Hands Down (Live)
| MTV Unplugged 2.0 | 2002 |
| Heaven Here
| Dusk And Summer | 2006 |
| Hey Girl
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Hold On (Bonus Track)
| The Swiss Army Romance | 2000 |
| I Light My Own Fires Now
| The Shade of Poison Trees | 2007 |
| If I Needed You
| The Wire Tapes | 2007 |
| If You Can't Leave It Be, Might as Well Make It Bleed
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Keep Watch for the Mines
| The Shade of Poison Trees | 2007 |
| Little Bombs
| The Shade of Poison Trees | 2007 |
| Living in Your Letters
| Summer's Kiss (EP) | 2002 |
| Living in Your Letters
| The Swiss Army Romance | 2000 |
| Living in Your Letters (Live)
| MTV Unplugged 2.0 | 2002 |
| Matters of Blood and Connection
| The Shade of Poison Trees | 2007 |
| Morning Calls
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Nightswimming
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Overkill
| The Wire Tapes | 2007 |
| Pretty Pathetic
| The Wire Tapes | 2007 |
| Rapid Hope Loss
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Reason to Believe
| Dusk And Summer | 2006 |
| Remember to Breathe
| So Impossible (EP) | 2001 |
| Remember to Breathe (Live)
| MTV Unplugged 2.0 | 2002 |
| Rooftops and Invitations
| Dusk And Summer | 2006 |
| Rooftops and Invitations (Live)
| AOL Sessions EP (iTunes Exclusive) | 2006 |
| Rooftops and Invitations (Live) (Video)
| AOL Sessions EP (iTunes Exclusive) | 2006 |
| Saints and Sailors
| The Places You Have Come to Fear the Most | 2001 |
| Saints and Sailors (Live)
| MTV Unplugged 2.0 | 2002 |
| Screaming Infidelities
| The Places You Have Come to Fear the Most | 2001 |
| Screaming Infidelities
| The Swiss Army Romance | 2000 |
| Screaming Infidelities (Live)
| MTV Unplugged 2.0 | 2002 |
| Several Ways to Die Trying
| A Mar, A Mission, A Brand, A Scar | 2003 |
| Shirts and Gloves
| The Swiss Army Romance | 2000 |
| Slow Decay
| Dusk And Summer | 2006 |
| So Beautiful
| A Mar, A Mission, A Brand, A Scar | 2003 |
| So Impossible
| So Impossible (EP) | 2001 |
| So Impossible (Live)
| MTV Unplugged 2.0 | 2002 |
| So Long, So Long (feat. Adam Duritz of Counting Crows)
| Dusk And Summer | 2006 |
| Standard Lines
| The Places You Have Come to Fear the Most | 2001 |
| Stolen (Acoustic Live)
| AOL Sessions EP (iTunes Exclusive) | 2006 |
| Stolen (Non-Juli Version)
| Dusk And Summer | 2006 |
| The Best Deceptions
| The Places You Have Come to Fear the Most | 2001 |
| The Best Deceptions (Live)
| MTV Unplugged 2.0 | 2002 |
| The Brilliant Dance
| The Places You Have Come to Fear the Most | 2001 |
| The Brilliant Dance (Live)
| MTV Unplugged 2.0 | 2002 |
| The End of an Anchor
| A Mar, A Mission, A Brand, A Scar | 2003 |
| The Good Fight
| The Places You Have Come to Fear the Most | 2001 |
| The Good Fight (Live)
| MTV Unplugged 2.0 | 2002 |
| The Only Gift I Need
| The Shade of Poison Trees | 2007 |
| The Places You Have Come to Fear the Most
| The Places You Have Come to Fear the Most | 2001 |
| The Places You Have Come to Fear the Most (Live)
| MTV Unplugged 2.0 | 2002 |
| The Rush
| The Shade of Poison Trees | 2007 |
| The Secret's in the Telling
| Dusk And Summer | 2006 |
| The Secret's In The Telling (Live)
| AOL Sessions EP (iTunes Exclusive) | 2006 |
| The Shade of Poison Trees
| The Shade of Poison Trees | 2007 |
| The Sharp Hint of New Tears
| Summer's Kiss (EP) | 2002 |
| The Sharp Hint of New Tears
| The Swiss Army Romance | 2000 |
| The Sharp Hint of New Tears (Live)
| MTV Unplugged 2.0 | 2002 |
| The Swiss Army Romance
| The Swiss Army Romance | 2000 |
| The Swiss Army Romance (Live)
| MTV Unplugged 2.0 | 2002 |
| The Widows Peak
| The Shade of Poison Trees | 2007 |
| Theme From Flood
| The Wire Tapes | 2007 |
| These Bones
| The Shade of Poison Trees | 2007 |
| Thick as Thieves
| The Shade of Poison Trees | 2007 |
| This Bitter Pill
| The Places You Have Come to Fear the Most | 2001 |
| This Is a Forgery (Bonus Track)
| The Swiss Army Romance | 2000 |
| This Old Wound
| A Mar, A Mission, A Brand, A Scar | 2003 |
| This Ruined Puzzle
| The Places You Have Come to Fear the Most | 2001 |
| Tonight I'll Take What I Can Get (iTunes Bonus Track)
| The Shade of Poison Trees | 2007 |
| Tonight I'll Take What I Can Get (Original Version)
| The Shade of Poison Trees | 2007 |
| Turpentine Chaser
| Summer's Kiss (EP) | 2002 |
| Turpentine Chaser
| The Swiss Army Romance | 2000 |
| Turpentine Chaser (Live)
| MTV Unplugged 2.0 | 2002 |
| Untitled (Hidden Track)
| The Swiss Army Romance | 2000 |
| Valens
| The Wire Tapes | 2007 |
| Vindicated (Hidden Track)
| Dusk And Summer | 2006 |
| Where There's Gold
| The Shade of Poison Trees | 2007 |
| Write It Out (Hidden Track)
| Dusk And Summer | 2006 |
