I won't defend my picks, since nobody else is defending theirs.
1. The Spirit Carries On
2. Metropolis Pt. 1
3. Six Degrees of Inner Turbulence (the whole suite)
4. The Count of Tuscany
5. Forsaken
6. Take the Time
7. Learning to Live
8. Pull Me Under
9. The Root of All Evil
10. Space Dye Vest
Honorable Mention: The remainder of Images and Words in its entirety (except Another Day); Caught In A Web, The Silent Man, Lifting Shadows Off A Dream, and Scarred; A Change of Seasons; Trial of Tears; most of the remainder of Scenes From A Memory; Blind Faith; As I Am, This Dying Soul and Endless Sacrifice, In the Presence of Enemies Pt. 1 and The Dark Eternal Night; A Nightmare to Remember; Bridges in the Sky; The Enemy Inside and Illumination Theory.
Finally, if part of a suite is presented as its own track number on a CD, it should be able to count as a song for this exercise. I only included all of Six Degrees because it is played live in its entirety (at least parts II. through VIII.), is presented as only one track on Score, and is brilliant from beginning to end.