Train of Thought is right up there with DT's best for me. DT's heavy side tends to come with mixed results, but they really nailed it on this album. One thing that makes it work is how raw this album is. There aren't a ton of guitar overdubs and multiple parts overcomplicating the music (Systematic Chaos). It's riff driven throughout and the proggy sections never feel out of place. JP is still innovating as a guitarist, experimenting with a different soloing style and also going all out with alternate tunings (3 of the songs are in C standard).
As I Am - As far as awesome openers go, this one is probably DT's Aces High. Seeing them open with this in 2010 with Maiden pretty much instantly made me a fan. Awesome riffs and they really nailed that proggy but Metal sound. Also one of my favorite Petrucci solos. There's a lot of shredding going on, but it's still pretty clearly well thought out. I also like that they didn't put a ton of rhythm guitar tracks underneath, really just sounds like the band jamming. The drum solo after seems to recall Tom Sawyer by Rush. Also JLB channeling James Hetfield.
Also like Ace's High, I find this song to be a step below most of the rest of the album. It's great live and a good way to start but the album really starts to pick up later on.
This Dying Soul - This is a song I'm conflicted on. I love the first half, at its best it is better than The Glass Prison. It manages to maintain the heaviness but it's significantly more melodic. A lot of the riffs introduced here would really become major themes for the rest of the suite. The verse riff for this song could probably be considered the "main riff" of the suite, as it shows up so much and is the basis for two songs (the other being Repentance). JLB also handles this song a bit better than TGP. Some really great guitar/keyboard leads throughout too. And that rhythm (which was apparently stolen from Ark) is awesome. Also love the piano playing on this, love when Rudess puts the synths away for a moment and does some acoustic piano stuff.
However, once it brings back that Glass Prison riff things kind of fall apart for me. The riff is awesome, as is the one that comes after, but something about this part just feels off. That odd time signature riff with all the vocal panning and effects just feels too much like a mess. I'm all for crazy polyrhythms and stuff but here it's a little too chaotic. There's too much going on. I also noticed during this listen that they really abuse the "shrink and grow" think. It's classic on Fatal Tragedy and also very cool on TGP but here it's starting to sound forced. Like they had to do something like that. I also dislike the solo section. Neither solos are bad but not very remarkable and the riffs underneath aren't as good. The unison at the end is impressive but feels tacked on. With that being said, if you edit the beginning of The Root of All Evil out and connect it to the end of TDS it actually makes for an effective transition.
So overall, it's a mixed bag. If it was just the first 6 minutes it would probably be my second favorite on the album, but the rest brings it down quite a bit. So it gets a vote.
Endless Sacrifice - The infamous Endless Wanking. This is the beginning of DT writing songs using the Maiden method of soft intro/heavy middle/soft outro. There seemed to be at least one on each album after this until Portnoy left, so I wonder if this was something he was fond of. Anyway, I really like this song and I think the instrumental section is awesome and gets a bit too much flak. There are so many awesome riffs in this song, starting with the chorus. That might be one of my favorite DT riffs. The way this song builds up is really cool too. The instrumental section doesn't just come out of nowhere, they build up to it and it flows really well. And again, the riffs underneath the solos are awesome. It gets a little proggy at times but I like that the entire instrumental is primarily riff driven, that doesn't happen often with DT. JR's keyboard melodies before his solos are mixed pretty low too which makes me think they wanted you to focus more on the riffs and the keyboard melodies were there more for effect. As for the actual keyboard solo, I think it's really good. The crazy sound effects at the beginning are cool. JP's solo is awesome. I love how he's going more for a shreddy thing here. He's still trying to do different things with his playing and I can appreciate that. He also shreds better than a lot of the shredders out there, so there's that. The twin lead that comes after the solos is like Maiden on steroids. And the riff that comes before the vocals return is pretty Maiden-esque as well IMO. Anyway, the twin thing to the end of the song is my favorite part of the song and really puts this one high in my rankings. Awesome riffs, great vocal delivery from JLB, and a crushing finale. Great song.
Honor Thy Father - Love this song. Never got the hate with it. It's like The Glass Prison, heavy throughout with a seemingly endless supply of awesome riffs. Not a lot to say about this song, it isn't very complicated, actually very simple for a DT song, but I get a lot of enjoyment out of it. The instrumental section is really interesting. There aren't any crazy unisons or proggy odd time signature riffs (although it goes back and forth from 6/8 to 5/8 a lot) and there's no guitar solo. Instead they seemed to try layering keyboard parts and playing with samples which is really cool. More about creating an atmosphere/mood than showing off technical abilities. It's one of the more dynamic DT instrumental sections and probably the single reason why I rank this song so high.
Vacant - A much needed break in the heaviness but probably among my least favorite DT ballads. I like how it's based on the Stream of Consciousness riff (or vice versa?) and there's nothing wrong with it overall but it doesn't really do anything for me beyond that. It's like they felt that they needed to put a ballad on the album and quickly wrote this. It gets a vote.
Stream of Consciousness - The only DT album where my favorite song is the instrumental. This song is so awesome, I like that they did it differently from their other instrumentals. Musically it's pretty simple but there are just so many cool riffs and melodies. I feel like this is the sort of thing Metallica was trying to do with that instrumental on Death Magnetic, just a cool showcase for riffs. DT does it far better though. Funnily enough, this song reminds me of Call of Ktulu at times, which is one of my favorite Metallica songs. This is also notable for having some really great solos from JP. Here he really merges his sense of melody and phrasing with the shreddy style he's maintained for the whole album. His second solo in particular is among my favorite moments on the album and the piano solo that comes after is pretty awesome too. I also like the Bach-esque rephrasing of the riff toward the end followed by the keyboard solo. Very Rick Wakeman like. The way it the parts layer at the end is almost too much for my ears to handle. In fact, DT (i.e. Portnoy) seem to really love the sudden endings (ala I Want You/She's So Heavy by the Beatles) and I actually think it would've been cool if this song ended that way. Just stop the song while the parts are being layered.
I would love to see DT write another instrumental like this and was slightly disappointed that Enigma Machine was less like this and more like Ytse Jam. I called The Dance of Eternity the best DT instrumental previously and I think I still stand by that, but this comes very close. Awesome stuff.
In the Name of God - This song feels like a bonus track to me. Something about it just feels really removed from the rest of the album. It's still heavy but a bit more on the proggy side and feels like the obligatory "epic" on an album full of similar length songs. That doesn't say anything about the quality of the song of course, just a thought about its place on the album. I still rank it very high. Again, great riffs and some really cool melodies. The other songs on this album tend to stay in one place and don't progress too much but this one really has a lot of twists and turns. It does really feel like an epic despite being on the shorter side of their modern epics. Really shows you don't need length to do something special. Also one of the best choruses in the DT catalog. The instrumental section is nuts, the unison is so frustratingly difficult that every time I attempt to learn it I have no idea how to approach it. It's also pretty unusual for JP being primarily legato when he tends to be all about alternate picking. Also interesting is that the keyboard solo has no guitar part under it. One of the few moments in a DT song where JP just stops playing for an extended period while the rest of the band continue (not counting times where the whole band stops and it's just one member). I wish he'd do that more. The riff coming out of the instrumental section never fails to get me pumped. The ending is epic. The woah oh oh's are straight out of the Maiden playbook. Again, we get a bit of restraint from JP just hanging on the chords while JR takes the lead on the piano. I also dig how they threw in The Battle Hymn of the Republic. Definitely would've been a cool song to see live.
Also, JR plays the final note with his nose.
Ranking:
1: Stream of Consciousness
2: In the Name of God
3: Honor Thy Father
4: Endless Sacrifice
5: As I Am
6: This Dying Soul
7: Vacant
and I want to be forever friends. 
Finally someone!!! 
), The Dance Of Eternity and The Spirit Carries On.
Blind Faith and Disappear are forgettable.
