Cloud Constructor is probably my favourite off the album, and not just for the "Shuffled" section (The CD is in my car so I can't check, but that's the bass harmonic bit, right?), although that is one of my favourite moments in all of music. As for least favourite, I would have to say Moving Spirit, at least overall. I love the solo (groove + wah = awesome, at least in this case), and there are parts that I really like, but overall I don't find it as interesting as the rest of the album. The vocal overlap/harmony bit at the end that Slope mentioned irritates me somewhat as well. Excessit, Insect and Fountainhead rule also.
EDIT: The beginning of Occam's Razor is rather cool as well, but overall I don't find it all that exciting. I'd love to see more Chapman Stick on the next album though, the potential of that instrument is amazing.