| Song | Year | Length | Track |
|---|---|---|---|
| 33 Flames for Mary | 2003 | 5:57 | 13 |
| 33 Shots at Louis | 2006 | 3:07 | 23 |
| 999 Escape | 2008 | 3:20 | 5 |
| A New Religion | 2006 | 4:11 | 25 |
| Anthem | 2003 | 4:39 | 14 |
| Ashes | 2008 | 1:16 | 8 |
| Believe | 2006 | 4:19 | 24 |
| Can’t Get My Mojo Risin’ | 2009 | 2:14 | 7 |
| Crimson, White, & Indigo | 2006 | 4:13 | 1 |
| The Cup | 2006 | 4:18 | 26 |
| Dawning of Decadence | 1998 | 2:18 | Bonus |
| Deuce | 2006 | 5:29 | 31 |
| Donovan’s Dread | 2005 | 3:16 | 15 |
| Donovan’s Dread (Live) | 2005 | 2:09 | Bonus |
| Song | Year | Length | Track |
| Elitist Lament | 2000 | 6:41 | Bonus |
| The Fool’s Overture | 2007 | 4:12 | 18 |
| Good Friday | 2002 | 7:50 | 10 |
| Half Hearted | 2007 | 4:52 | 32 |
| Here On the Beach | 2006 | 3:00 | 29 |
| I Don’t Want to Live Without It | 2004 | 3:13 | Bonus |
| Keep Doing What You Do | 2006 | 5:04 | 20 |
| The Last Man to Walk Alone | 2006 | 3:49 | 21 |
| Long Way Home | 2007 | 6:03 | 33 |
| Long Way Home (Original Version) | 2007 | 6:14 | Bonus |
| Lorelei | 2004 | 6:30 | 12 |
| Naked | 2006 | 4:35 | 30 |
| The Old Man In the Sea | 2006 | 3:54 | 27 |
| One | 2004 | 5:47 | 17 |
| Song | Year | Length | Track |
| Paradise | 2004 | 3:20 | Bonus |
| Peace | 2005 | 4:45 | 16 |
| Perfect Light | 2004 | 4:26 | 11 |
| The Phoenix | 2004 | 3:56 | 9 |
| Princess of Pearl Avenue | 2006 | 4:22 | 4 |
| Rubicon | 2009 | 2:33 | 3 |
| Rubicon (Live) | 2009 | 2:42 | Bonus |
| She Said | 2006 | 3:09 | 19 |
| Sister Josephine | 2008 | 4:32 | 2 |
| Song For Diane (Don’t Give Up) | 2008 | 3:28 | Bonus |
| Speak No Evil | 2004 | 2:45 | Bonus |
| Tommy’s Got a Gun | 2008 | 3:09 | 6 |
| Twilight Of Innocence | 1997 | 7:02 | 28 |
| Welcome Home | 1998 | 3:17 | Bonus |
| You Sure Were Fun | 2005 | 4:16 | 22 |