Alright, I made a full song list and gave it a 0 to 100 (actually 50 to 100) score and then got the average score for each album. This is what I got:
A Change of Seasons 95 (not including covers)
Scenes from a Memory 91,33
Six Degrees of Inner Turbulence 87,5
Images & Words 86,25
Train of Thought 86
Black Clouds & Silver Linings 82,67
Octavarium 79,38
Systematic Chaos 77,38
Falling Into Infinity 76,73
Awake 76,64
Going by gut feeling however (sometimes great songs more than compensate for crappy songs in the same album) this is what I have:
Scenes from a memory
Images and Words
Six degrees of inner turbulence
A change of seasons
Black clouds and silver linings
Awake
Octavarium
Train of Thought
Falling into Infinity
Systematic chaos