"Metropolis Pt. 1," as everyone has said, is pretty much THE Dream Theater song. All of their best qualities are in it: memorable solo sections, epic ending, soaring vocals from James, Myung bass solo, Mike's cool intricate drumming, the intro (including the pretty simple but instantly recognizable riff. You know the one), and the seamless transition from verse to big instrumental section, which seems to be overlooked a lot sometimes (I'm looking at you Scarred). Its not my favorite song by DT, and I'm not even sure if it would be in my top ten, but it really is a great song.
@m0hawk: Apparently the only thing separating "retro DT" from "latter DT" is one studio album? Get Score. James sounds fantastic, you get to hear "6DoiT," "Octavarium," "Sacrificed Sons," and "Metropolis" with an orchestra, not to mention "Under a Glass Moon," "Raise the Knife," and "The Spirit Carries On."