I LOVE this song! Especially where James takes it at the end. Yes, it is a little sad, but it is a very honest song, emotionally. I work at a local radio station two nights a week, and I always end the night with "Beneath the Surface" one night, and "The Spirit Carries On" the next night. One night on a sad note, the next on a hopeful one. Plus, hopefully I'm making a few new Dream Theater fans!
Like several posters have said, there are so many great ones, how do you pick? Most of my favorites have been mentioned already, but one of the ones I just can't get enough of listening to that nobody has mentioned so far is Peruvian Skies. James's voice, the slow buildup, and finally the all out crunch of the song blow me away. I also like Forsaken. Can't help it, I love the piano intro and outro, and Petrucci's riffing in that song. And again, Jame's voice when he screams out "I have to know your name...Where have I seen your face before?" I get chills thinking about it now.