I was listening to Misunderstood while walking earlier, and it still has that je ne sais quoi to it, probably more so than any other DT song. Particularly the entire "second verse" section, with the little reverse bits in the background, and Portnoy's little rototom fills, Myung's bass, the snare hits echoing off in alternating stereo channels, then that little injection of feedback from Petrucci before the full band kicks in on the chorus.
Most DT songs you "get used to", in a sense. Misunderstood still holds some of that "shock value" (for want of a better term) for me, some 8 years after first hearing it. And we haven't even dealt with that mindbending coda. A song that leaves me in awe.