Bands in no particular order. Top 3 songs (in order) for each.
Dream Theater - Metropolis part 1, Voices, In the Name of God
Porcupine Tree - Deadwing, Trains, Dark Matter
Devin Townsend - Earth Day, Deadhead, Seventh Wave
Ayreon - The Sixth Extinction, Age of Shadows, Day 3: Pain
Opeth - Bleak, Blackwater Park, The Drapery Falls (derp, all BWP)
Coheed and Cambria - The Light & the Glass, In Keeping Secrets of Silent Earth: 3, Mother Superior
Pain of Salvation - A Trace of Blood, Idioglossia, Iter Impius
Tool - Vicarious, Rosetta Stoned, Lateralus
Between the Buried and Me - White Walls, Sun of Nothing, Disease Injury Madness
Pink Floyd - Echoes, Comfortably Numb, Us and Them
Bonus:
Green Carnation - Light of Day Day of Darkness, Lullaby in Winter, Crushed to Dust