| Rank | Song | Count | Graph |
|---|
| 1 | Pull Me Under | 21 |  |
| 2 | As I Am | 4 | |
| 3 | Disappear | 4 | |
| 4 | Endless Sacrifice | 4 | |
| 5 | Hollow Years | 4 | |
| 6 | The Test That Stumped Them All | 4 | |
| 7 | 2285 Entr'acte | 3 | |
| 8 | A Life Left Behind | 3 | |
| 9 | A New Beginning | 3 | |
| 10 | A Savior In the Square | 3 | |
| 11 | A Tempting Offer | 3 | |
| 12 | A View from the Top of the World | 3 | |
| 13 | Act of Faythe | 3 | |
| 14 | Answering the Call | 3 | |
| 15 | Astonishing | 3 | |
| 16 | Awaken the Master | 3 | |
| 17 | Begin Again | 3 | |
| 18 | Beyond This Life | 3 | |
| 19 | Brother, Can You Hear Me? | 3 | |
| 20 | Chosen | 3 | |
| 21 | Digital Discord | 3 | |
| 22 | Goodnight Kiss | 3 | |
| 23 | Heaven's Cove | 3 | |
| 24 | Hymn of a Thousand Voices | 3 | |
| 25 | In The Name Of God | 3 | |
| 26 | Instrumedley | 3 | |
| 27 | Invisible Monster | 3 | |
| 28 | Keyboard Solo | 3 | |
| 29 | Lord Nafaryus | 3 | |
| 30 | Losing Faythe | 3 | |
| 31 | Machine Chatter | 3 | |
| 32 | Moment of Betrayal | 3 | |
| 33 | My Last Farewell | 3 | |
| 34 | New Millennium | 3 | |
| 35 | Only A Matter Of Time | 3 | |
| 36 | Our New World | 3 | |
| 37 | Power Down | 3 | |
| 38 | Ravenskill | 3 | |
| 39 | Sleeping Giant | 3 | |
| 40 | Solitary Shell | 3 | |
| 41 | Stream Of Consciousness | 3 | |
| 42 | The Alien | 3 | |
| 43 | The Hovering Sojourn | 3 | |
| 44 | The Path That Divides | 3 | |
| 45 | The Road to Revolution | 3 | |
| 46 | The Walking Shadow | 3 | |
| 47 | The X Aspect | 3 | |
| 48 | This Dying Soul | 3 | |
| 49 | Three Days | 3 | |
| 50 | Transcending Time | 3 | |
| 51 | Trial Of Tears | 3 | |
| 52 | War Inside My Head | 3 | |
| 53 | When Your Time Has Come | 3 | |
| 54 | Whispers On the Wind | 3 | |
| 55 | A Better Life | 2 | |
| 56 | Descent of the Nomacs | 2 | |
| 57 | Dystopian Overture | 2 | |
| 58 | The Answer | 2 | |
| 59 | The Gift of Music | 2 | |
| 60 | Another Day | 1 | |
| 61 | Another Day (2007 Remix) | 1 | |
| 62 | Home (Edited Version) | 1 | |
| 63 | I Walk Beside You | 1 | |
| 64 | Learning To Live | 1 | |
| 65 | Lie (Edited Version) | 1 | |
| 66 | Lifting Shadows Off A Dream | 1 | |
| 67 | Metropolis, Pt. 1: The Miracle And The Sleeper | 1 | |
| 68 | Misunderstood (Edited Version) | 1 | |
| 69 | Peruvian Skies | 1 | |
| 70 | Pull Me Under (2007 Remix) | 1 | |
| 71 | Sacrificed Sons | 1 | |
| 72 | Solitary Shell (Edited Version) | 1 | |
| 73 | Surrounded | 1 | |
| 74 | Take The Time | 1 | |
| 75 | Take The Time (2007 Remix) | 1 | |
| 76 | The Answer Lies Within | 1 | |
| 77 | The Root Of All Evil | 1 | |
| 78 | The Silent Man | 1 | |
| 79 | The Spirit Carries On | 1 | |
| 80 | Through Her Eyes (Alternate Album Mix) | 1 | |
| 81 | To Live Forever | 1 | |
| 82 | Under A Glass Moon | 1 | |
| 83 | Wait For Sleep | 1 | |