Hm... just using the 6 presented in the OP.
#6. Illumination Theory
This song is disjointed to me. It has some cool ideas, but it doesn't flow well between sections - the orchestral section in the middle just doesn't fit, the transitions in and out don't work to me. The tag at the end of the song is a bit annoying when it comes on shuffle. I don't like the nebulous lyrics, the production, or the riffs, and in fact the only thing I really like about this is the amazing epic build into the last verses. Mangini's fills, that driving kick drum on the beat, the crack of those toms or whatever he's hitting - magical. Unfortunately that's the only thing I really like about this song.
#5. In The Presence of Enemies
Some great music in this song across both parts. For part 1 I really like the riff and just how the band works so well. I love the tension in those really fast chromatic runs leading up to the main motif. Lyrically I like the idea behind all of it, too; I don't find it nearly as corny as some people do, or as cheesy as the inspirational ballads they'd do in later years. One of my favorite DT sections ever is the beginning of part 2, with the creepy bass and piano, and James giving an awesome vocal performance. I really love the "I cannot see his face, but I can feel his spite" part, his voice is great. Lots of shred on this but I think it's a lovely epic that usually - not always, but usually - remains entertaining throughout.
#4. The Count of Tuscany
Beautiful. Sweet, beautiful music. One of DT's finest opening few minutes in an epic. Production is great. Lyrics aren't Shakespeare but they work for a song like this. Petrucci in rare form, from the solos to the riffs to the spacey section to the clean strumming at the end. Jordan does some really cool things, I like the synth part in the first half that just uses 2 notes. This song really has everything DT does well in the back half of their career, it's just a delight from start to finish, bursting with melody and creative ideas.
#3. A Change of Seasons
Incredible. What more can be said about ACOS? First time I heard The Crimson Sunset is one of those pivotal moments in my musical life. Still one of their best songs ever.
#2. Six Degrees of Inner Turbulence
I personally do count this as one long song with 8 individual parts, and it's phenomenal in every way. Every member of the band has at least a few moments throughout this track that rank among their best stuff ever in this band. It's a brilliant work of art, and each musician is firing on all cylinders. It's only a hair away from #1.
#1. Octavarium
It does not get better than this. The nuggets referencing so much inspirational music and so many artists, the musical nuggets alone referencing the scale system and the rest of the album, the story about a man waking from a coma, the Continuum and the Pink Floyd homage, the excellent lyrics particularly in the Razor's Edge section, John Myung's best bass line ever, Jordan Rudess's best keyboard solo ever, I could go on and on and on. AMAZING.