For my favorite, I may have to go with Wake of Magellan. That could change depending on the day of the week, or my mood, or the weather, but overall it's probably the one that gets me going "wow" consistently. The counterpoint at the end needs listened to 3 or 4 times before it really starts to get you but it's one of the most amazing pieces of music I've ever heard. Even better when heard in context of the whole album, as it is sort of the climax of the whole story.
Everyone really should give this a listen, particularly the end of the song. If you listen to nothing else in this thread, you should listen to this song from 2:45 on to the end IMO.