It's tough for anything to contend with "The Spirit Carries On". It's truly an emotional roller coaster that's attached to their greatest album, in my opinion.
For me though, the one that really tugs at my heartstrings, is "Disappear". It has this spiraling darkness to it, and the message feels very real - that sense of hopelessness and questioning without getting the answers that you really hope for. It comes across as someone being trapped, reaching for some sense of resolve that just isn't there.
Life isn't always a bouquet of roses, and Dream Theater really portrayed that well with this song.