Some stuff I realized:
I think Petrucci once said that the similarity between Trial Of Tears and In The Dead Of Night was on purpose and that the solo was supposed to be a Alan Holdsworth homage.
I find these two parts have similar harmonic progressions:
The Shaman's Trance (Bridges In The Sky) - 2:55
Fatal Tragedy - 2:24
Also, the main theme from SDOIT reminds me of this:
https://www.youtube.com/watch?v=SBMsulQMqm8 - 3:34
The beginning of The Root Of All Evil ist very similar to Pink Floyd's Welcome To The Machine, ESPECIALLY the Score version.
This is not really a nugget, but since it's been talked about already: Cutting off Pull Me Under and the reverse sounding solo in Misunderstood are two techniques The Beatles used in I Want You (She's So Heavy) and I'm Only Sleeping.
Solitary Shell reminds me a lot of Solsbury Hill, because of the similar names and the 7/4.
Anyone noticed the last, VERY quiet piano note at the end of In The Name Of God? (this one is kinda obvious, ik)
And of course, Octavarium:
The intro is clearly a homage to Shine On You Crazy Diamond.
6:35 sounds a lot like Bohemian Rhapsody to me.
9:05 has a similar harmonic progression like Anna Lee.
11:40 is referring to Echoes by Pink Floyd (like already Phantom Of The Opera did)