Once again, there is not a single weak song, here. In the Presence of Enemies pt. 2 is the closest, and it's still badical. (Meanwhile, in the other thread, In the Presence of Enemies pt. 1 was my vote for "Best opener." Weird!)
Illumination Theory is my favourite song of those listed. Octavarium's the best, but Illumination Theory's my favourite. I think In the Name of God is probably the strongest closer - it's bonechillingly epic in a way that doesn't sound like any of their other songs, and the end of Illumination Theory is epic in a way they do quite frequently, but they'd never done it as well as Illumination Theory until... well, until Illumination Theory!
Razor's Edge is strong, too, but y'know. Burnout! The Count of Tuscany (which I'm listening to right now, and love more than I ever remember) is a long song on an album full of them, so it's not as significant as part of the story. Illumination Theory feels like a huge sigh after the brevity of the rest of the album, whereas The Count of Tuscany is just the long song that happens to be up last. It does end so, so well though. I always remember it as ending acoustically, which means I'm always pleasantly surprised by the way it builds into something much bigger. Space-Dye Vest and Beneath the Surface are very different but while they end each album quietly, they do so in an interesting and engaging way, and I cherish them both. Most days, Beneath the Surface is my favourite song on A Dramatic Turn of Events.