Actually some of these you've ranked were written as one song.
I'm amazed that you left out In the Presence of Enemies!
Here's my ranking anyway
1.- Octavarium: Personally, the best song by DT ever, and yeah, this kicks Metropolis's ass for me because it does so many things so good, idk, my fav song by DT ever. Kicked ass, kicks ass, and will kick ass.
2.- Now, for Metropolis. I do count Metropolis Pt2 as a single song split in parts. But I can't count Metropolis Pt 1 as anything else as a prequel and overall different material, even though many things are reprised in Pt2. Beautifully written and filled with energy, as well as having some of the best segments in DT discography.
3.- 6DOIT: This one is one song, longest OFFICIAL song in DT discography. I love it, absolutely love it. Especially the Score version. Emotive, great, deals with a topic that I'm very interested on, awesome. The only letdown is probably the fact that I'm not very fan of the studio version and how short War Inside my Head is, but everywhere else, it's awesome.
4.- In the Presence of Enemies: The ultimate DT Epic. It has been proven, by people who have actually covered it, that this is the single most difficult piece ever written by DT. And if not, at least it's the hardest epic. It puts everything that DT is in a single song, melodic calm parts, epic choruses and extremely agressive and crazy hard solos. Telling an awesome story. My issue with this? Nothing, not really.
5.- Twelve Step Suite: The band did see it as a single song (or work) spread across 5 albums. And it's the longest song NONOFICIALLY in DT discography. A total carnage heavyfest for any metalhead, nearly completely heavy from beggining to end, except for Repentance which does a great job being a letdown but halfway, stops being really calm and slowly returns to the kickassery of TSF. MY GREATEST PROBLEM: The lyrics. Sure, it has some nice parts here and there, especially in TGP, but god, TSF isn't a good song lyrically. "I am responsible, when anyone..." sure, that fits as a promise by an AA member, but not as a line in a metal song.
6.- A Mind Beside Itself: Listen to the LSFNY version. They do an awesome job in placing it all together as one piece and it flows perfectly into The Silent Man. My greatest issue is actually Erotomania, don't get me wrong, love the second half of it, but at the beggining it's actually pretty random and not very attractive for me. Voices is perfect.
7.- Illumination Theory: Love it as well. My issue? Too much time without DT main members, too little lyrics and very long solo section which really doesn't add that much. Ending is beautiful and perfect and the piano passage at the veery end is also awesome. The intro really does an incredible job. Best song on DT12 for me, and has very meaningful lyrics that could be adapted into something bigger.
8.- The Count of Tuscany: Beautiful intro, the best on DT has ever done. Beautiful outro, awesome as well. The issue? The middle part, as well as the verses and chorus, are rather weak and feel not soo inspired as the intro. The enormous silent part is mood-dependant, sometimes I want to hear it, others I just skip it, and that's not something good.
9.- A Change of Season: My least favorite DT epic. Probably because of how much I hate the studio version and just... I don't know, it doesn't feel... cool. I cannot say I love it, but I cannot say I don't like it, it's just... Meh, well, I can't say anything else.