I'm going to reply before reading anything past the first couple of posts so as to not influence my ranking decisions...though these could fluctuate with the phases of the moon, so it's not set into stone.
01. Xanadu
02. La Villa Strangiato
03. 2112
04. Cygnus X-1, Book I: The Voyage
05. Cygnus X-1, Book II: Hemispheres
06. Natural Science
07. By-Tor & The Snow Dog
08. The Necromancer
09. The Camera Eye
10. The Fountain Of Lamneth
Considering how much I *LOVE* the run of 2112-AFTK-HEMI, those songs HAD to make up my top 5. "Natural Science" is an easy next because of just how heavy and rocking that song is, especially the beginning. After that, having "By-Tor" and "Necromancer" come next because of the earlier epics, those are my favorites from the first three albums. I never really LOVED "The Camera Eye", it has some neat ideas and holds together well enough (in a "Xanadu"-ish sort of way, with two major parts with different lyrics after a lengthy intro), but I at least like it a bit more than TFOL, which also has some neat ideas, but its disjointedness means it falls to tenth place.
Honorable mention to "Jacob's Ladder", for being an amazing mini-epic at nearly seven and a half minutes, which I would rank between 6th and 7th place if it were included.
-Marc.