Under A Glass Moon is rather low on my list as well, but both TTT and UAGM are still good songs. They're just not as good, for Dream Theater's standards.
The Mirror is much better than Lie, but even then, I still like Lie. As for HTF, I wouldn't even call it outright bad, but it's still the bottom of my list by a pretty significant margin. Runner-ups are JLMB and the aforementioned Peruvian Skies. So yeah, as you can tell, I think even the worst of Dream Theater is still alright in some way. TTT may be 15 away from the bottom, but it's still a very good song; just heavily outclassed by many other DT songs.
I honestly don't like The Mirror (and, to a lesser extent, Lie). If I'm listening to Awake, I'll skip both. Of course, in the grand scheme of music, they're not bad songs, but, as you said, heavily outclassed by many other DT songs.
As far as instrumentals, SOC is my undisputed favorite (although the slow section toward the end does bog it down a bit).
Ytse Jam gets 4/5 (esp. considering when it was written)
Erotomania gets 3.5/5 (never been a favorite of mine)
Hell's Kitchen gets 4/5 (but for completely different reasons)
Dance of Eternity is a very close runner up to SOC - minimum of 4.5/5
Enigma Machine is 3.5/5
I'm not considering Overture 1928 outside the context of SFAM, but it would get 4.5/5 if I did. Nor am I considering False Awakening Suite or the SDOIT Overture (the former not really being a band track).
Eve is fine, but it doesn't compare to the rest. I think I've heard Raw Dog maybe twice, and I wasn't impressed.