There's quite a few on here that I am not familiar with, and from the bands I *am* familiar with, you picked some of the not-so-obvious choices (Gates instead of CTTE, Duel instead of Stranger, The Water instead of Great Nothing, etc.), so this was a bit difficult at first, but here's my seven picks:
Transatlantic's "Duel With The Devil" - While just a step below SIYS for best TA epic for me, this still has some amazing moments throughout, and is a killer way to open Bridge Across Forever! Not many bands in prog would open their second album with a 26-minute epic, but they did it expertly!
The Flower Kings' "The Truth Will Set You Free" - And on the subject of album-opening epics, this one is King. This ambitious piece opens what would become one of the band's most ambitious albums, and this epic does not hold back! One of my favorite TFK epics from a Top 3 TFK album!
Frost*'s "Milliontown" - When Frost* debuted, their first album was one that got a LOT of spins, mostly because of this epic. I haven't heard an epic quite like this one from many bands, and so it stands out as one of the best epics of this century to my ears.
Genesis' "Supper's Ready" - "Walking across the sitting room..." - such a powerful tune, and without this piece, a lot of modern prog epics probably would not sound the same. I think the idea of progressive rock epics in the symponic prog subgenre owe a lot to this one, but even among all that have come since then, this one still stands the test of time.
Spock's Beard's "The Water" - Not the obvious SB epic to pick, but this one is full of raw and youthful energy, and having recently listened to the album (and the live version of this song on "The Beard Is Out There"), I have renewed interest in this epic. It's quite different from anything Neal has written since then, but still has a lot of his unique touches throughout.
Haken's "Visions" - When I was getting into Haken, this was one of the first songs that connected with me, and I fell in love with the piece, especially the epic ending that soars and feels like an immense release. This one gives me musical goosebumps every time I get to the end.
Yes's "Gates Of Delirium" - Like with others, this wouldn't seem to be the obvious Yes epic pick (some would say "Ritual" or "Close To The Edge" would be better), but this one stands out as it was the only album with Patrick Moraz, and his involvement with Yes really took their sound into new and interesting directions, the least of which helped create this sprawling war-influenced epic, which closes with one of the most hauntingly beautiful endings to an epic ever.
And since 7 is an odd number to pick, here are three honorable mentions/close-picks:
ELP's "Tarkus" - Now, of the classic prog bands here, this is one I *would* expect to see on a list of epics, but it didn't quite make my cut. I like it, but it's not an epic I put on very often. Still really great, though, and you gotta love that fast riff in 5. (Also, Jordan Rudess' cover of this is FANTASTIC)
IQ's "Harvest Of Souls" - Yeah, it's very derivative of "Supper's Ready", but so what? IQ rock this one really hard and it's got some of their own spins on old ideas. Basically, if Genesis were a 2000's prog band, this is probably what it would have sounded like, and that's not necessarily a bad thing!
Symphony X's "The Odyssey" - I started in on SX *after* I got into DT, and I think because of that, I never really got into SX as deeply as I did with DT, but "The Odyssey" is one of the best songs I've ever heard and I love what they do with it. Side-note, I once witnessed a high school marching band do a field show based on "The Odyssey" and it was awesome seeing them march in the odd-meters and play some of that great music in a live setting with real horns!
-Marc.