This is a tough one. For me it's their second best album (after SFAM).
Disc one is absolutely superb from start to finish, as consistent a disc as you could ever hope for. I think I prefer this disc - all the songs are great. Whilst the suite is absolutely outstanding in some sections, for me the piece as a whole is a little lacking. Despite this, the very best parts are the better than any other on either disc. If the suite had been broken down into it's various parts my favourite track on the album would have been easy - The Test That Stumped Them All. The suite builds fabulously up to that point but the rest of it from then onwards is not as good, IMHO.
I thought seriously about The Great Debate and Blind Faith (why doesn't Labrie contribute more lyrics, his are good?) but eventually went for The Glass Prison. I'm a little biased, but that's the first DT track I ever heard.