For comparison, here is mine, with a bit of reasoning:
This is very interesting to read (and I agree far more conducive to discussion than just a bare ranking). I'll give it a whirl.
1. SFAM -- It has everything that makes DT great and very little that I don't like. It is, of course, an epic concept album. It has extremely heavy parts (Beyond This Life). It has great prog epics (Home). It has ballads (TSCO). It has great stand alone songs (Fatal Tragedy). It has an amazing instrumental, which, while perhaps being the most over the top examples of prog wankery, manages not to sound like wankery. And it has a cool story (regardless of it perhaps being derivative of what I think is a rather lackluster movie). It also benefits from being preceded by a relatively mediocre album.
2. I&W -- It's the original. When I heard this album, I was in a period of musical despondency. Fates Warning was really the only band making what I considered to be GREAT music. Queensryche was on a downturn. Rush had recently released what I typically consider to be the band's worst album. Halford had left Judas Priest. Fear of the Dark was better than Maiden's prior album, but it still wasn't as good their earlier albums. My own band had broken up after having started down a road that I like to think would have had us making music similar to that of DT. I heard songs like Metropolis and Learning to Live and thought they were just about perfect. Some days, this is #1. Some days, it could drop to #3, but never lower than that.
3. SDOIT -- This album's biggest challenge was that it was a follow up to SFAM. I didn't really like disc one at first, and I still consider Disappear and The Great Debate to be throw-away tracks. The rest of disc one is great, however. The Glass Prison kicks ass. Blind Faith is one of my favorite all time DT songs, and Misunstood has a very cool vibe. The title track almost stands on the same footing as SFAM. It was amazing to hear what is, at bottom, a metal band come up with something that, in many ways, rivals some of the greatest classical works and rock concept albums of all time.
4. Awake -- Awake had the challenge of following up I&W, and it didn't do as well as SDOIT did following SFAM. Innocence Faded is one of DT's weakest songs, and I hardly ever listed to Lie or The Mirror. The rest of the album is really good, however.
5. Train of Thought -- There are a lot of analogies between ToT and Awake. This Dying Soul and Honor Thy Father are, in my view, much weaker versions of As I Am. Stream of Consciousness is probably my favorite DT instrumental.
6. Octavarium -- A good follow up to ToT, with it's more prog feel. Most of MP's "nuggets" are lost on me, and I Walk Beside You is on the same level as Innocence Faded in terms of weak DT songs. I LOVE Panic Attack, and the title epic is Amazing (especially the second half). It's even good in the sped up 3x version that's on YouTube somewhere.
We now get into albums that all have some fairly major weak points.
7. DT12 -- Illumination Theory is one of DT's greatest epics. I love The Looking Glass and Along for the Ride. Enigma Machine is cool, but not up with their best instrumentals. The rest of the album is very take-it-or-leave-it.
8. ADTOE -- Very similar to DT12 in terms of overall feeling. I love Breaking All Illusions and, to a somewhat lesser extent, Bridges in the Sky and Outcry. I feel like I should like Lost Not Forgotten better than I do, but I don't. The rest of the album is somewhat lackluster.
9. BC&SL -- This should have been a great album and it wasn't, so it suffers for that reason alone. A Nightmare to Remember is too Long. A Rite of Passage is just ok. I love Wither. The guitar player in my old band had written a song about the same topic, which I thought was really clever. Shattered Fortress is good, but it's largely retread. TCoT really good, and I just don't get all the love for The Best of Times.
10. FII -- I really wanted to love this album so much. I remember listening for the first time, just waiting for something that made me say "wow!" but that never came. I think Hollow Years was my favorite song at first. I occasionally listen to the whole thing, but the only songs that really grab me anymore are Hollow Years, Hell's Kitchen, Anna Lee and Trial of Tears.
11. WDADU -- As flawed as this album is, it was a GREAT debut album, and it has some great moments. Had I heard it when it was released, I think I would have loved it. Ytse Jam is an amazing piece of musicianship for a bunch of guys who were barely 21 (same age as me) when they recorded it. The Killing Hand and Only a Matter of Time remain strong.
12. Systematic Chaos -- Another one that I feel like I should like more than I do. Admittedly, they were due for a letdown, but.... Repentance and Ministry of Lost Souls are songs I'll probably never listen to unless I try to make an attempt to give the album another shot. ITPOE has some good parts, but it's ultimately too long and disjointed. When I first heard the intro, I was excited, and then it got to the hyper-wank section and never pulled out of the nosedive. Forsaken seems like a bad attempt at a commercial song. Constant Motion is really the only song I like.
As mentioned earlier and in other threads, I've probably listened to the Astonishing three times all the way through, and it's never hooked me in any way that makes me want to dive in deeper, so I don't think I can fairly rank it. I probably felt the same way about Tales from Topographic Oceans after the first few listens, but now I probably rank it in the top 4 for Yes albums, so you never know.