I didn't really bother to read everyone's comments, but here's my two cents:
Just so you know where I'm coming from: I first became a DT fan with Octavarium, my second album being Awake (and then I don't remember anymore). Both SC and BC&SL are more up than down in my rankings (certainly over FII, WDADU, Awake, Train of Thought, competitive with the rest, excepting SFAM and maybe SDIT).
On the individual songs: Both ItPoE and CoT are amongs my top 10 DT songs, I love Wither and The Best of Times, actually find The Shattered Fortress the best part of the AA Suite, followed by Repentance. I also like The Ministry of Lost Souls quite a lot (though the instrumental section in the middle is somewhat unnecessary/out of place). The rest of the albums is, in my opinion, also pretty solid, excepting Constant Motion...
All in all, I think the problem with "underrated" DT albums or even songs is that they have produced so much that is so good that the standards have become too high.