The prog-snob in me picked "Illumination Theory", being the long epic of the album, and I really REALLY do love it, but the shorter songs are pretty good, too.
I will say, though, at the moment, I know that the two instrumentals aren't near the top, and "Along For The Ride" and "The Enemy Inside" are in the middle, and not just because they were pre-released as singles, but I just find that the others are as good if not a bit better than them, although TEI still blows me away.
I'd have to give props to "Behind The Veil" and "The Bigger Picture", and I love the Rush-feel of "The Looking Glass" and "Surrender To Reason".
Honestly, there's a LOT to like about each song, but as it stands, I'd say TI is still at the top, and it probably will remain there for awhile.
-Marc.