As for me, I'd say, by album,
(I need to listen to When Day and Dream Unite a LOT more to form opinions)
"Pull Me Under." I usually just skip to at least "Take the time," but when I got the Greatest Hit collection with the remaster, I actually really listened to this song, and I felt nostalgia. I fell in love again. But this song's right at the start, where you can easily skip it and not have flow ruined later on.
"Under a Glass Moon." In between "Metropolis, pt. 1" and "Wait for Sleep/Learning to Live" is one of the most badass metal songs from the nineties.
"Innocence Faded." I tend to skip the second two songs, or more frequently the first three, of Awake. But after watching Score, I noticed how much I really loved the ending to this song. It's beautiful, and right before "A Mind Beside Itself!"
"Scarred," for reasons I'm sure everyone else empathizes with.
(I need to listen to Falling into Infinity a LOT more to formulate opinions on it.)
"Beyond This Life." Between "Fatal Tragedy" and "Hom--"wait. Uh.. well, between "Fatal Tragedy," and (skipping the song directly after) "Home?" Hard to remember this song. Plus, of all Dream Theater songs, this just feels like it goes on and on. But the Budokan performance was utterly phenomenal, and I play that live version all the time.
"The Dance of Eternity." I mean, it's a beautiful song and all, but when I listen to this album, I go straight from "Home" to "Finally Free." At least, I used to. Now I listen to "The Dance of Eternity," because it is just awesome.
"Blind Faith," when I first got Six Degrees, was just "that song between 'The Glass Prison' and all the other awesome songs." But one day, I realized I didn't really know much about this song, and I realized I was in love with the album but I clearly didn't know this song, so I sat down and listened to it, and I've been a massive fan ever since.
"Disappear" was always just "the interlude" to me. It's the breather between Disc One and Disc Two. But one day, I also sat down and listened to this, and I learned to truly appreciate the beauty of it. I think it was the same day I found out what it was about. Now Six Degrees is a perfect album in my eyes.
"This Dying Soul" was "the song between 'As I Am' and 'Endless Sacrifice'" for a while. It felt like I didn't really "get" it. But when I started to appreciate the Twelve-Step Suite as a whole, when I started counting this song not as one song but as two individual movements that are completely separate musically, I saw the beauty of it. And now this is one of my most-favourite songs of all time.
"The Answer Lies Within" was "the song between 'The Root of All Evil' and 'These Walls'" for a while. But then I heard Jordan Rudess' cover off of Notes on a Dream. I found myself enjoying the melody, singing along, and I genuinely had fun listening to it. Then I listened to the real song again, and I felt such a surge of joy. This song is a classic. ;w;
"Sacrificed Sons" was "that one really slow 9/11 song made four years late, in between 'Never Enough' and 'Octavarium'" for a while. Hell, even up until pretty recently. It was watching Score for a third time that got me to fall in love with the song.
"Repentance" was "that one really slow song in between 'The Dark Eternal Greatest Instrumental Section Ever' and 'Prophets of Really Awesome Song.'" But I think it was around the same time I started appreciating "This Dying Soul," when I started counting the Twelve-Step Suite by their individual movements instead of their tracks, that was when I saw the fucking beauty to this, as well. The ninth movement is still one of my favourite anythings of anything ever.
Pretty much everything on Black Clouds that wasn't "The Shattered Fortress" or "The Count of Tuscany" was "one of the songs that's not 'The Shattered Fortress' or 'The Count of Tuscany'" until I'd had enough time pass to listen to the album with a sense of nostalgia. "A Nightmare to Remember" is now sixteen brilliant minutes of amazing flow, "A Rite of Passage" is eight minutes of yes yes yes yes yes, "Wither" is the most badass I've ever seen anyone describe writer's block (and the piano cover on the EP adds new layers to the beauty!), and "The Best of Times" is unadulterated beauty. Hell, I also got a newfound appreciation for "The Shattered Fortress" when I did that whole "they're individual movements, not songs" thing.
Pretty much every song I didn't mention except for most of Metropolis, pt. 2 or "The Ministry of Lost Souls?" I always loved them so much. ;w; The aforementioned album and song? Meh. >.>