prog metal by what definitions?
I mean if I can list bands like Summoning, it would be impossible
But, I'll go with my own definition I suppose, whatever that is.
I'll also add some commentary. You know, perhaps making things a little interesting
Since it's a "top albums", I must exclude albums with obvious weak parts, like Beyond Twilight - Section X for instance. Extremely inconsistent album, but very good when it's good.
I consider Porcupine Tree, Oceanzise, Ulver and a few others to be 'regular' prog rock, and not really metal. I dunno why, I just draw the line somewhere I guess. Otherwise I'd have to put King Crimson here cuz they can be just as heavy, and in that case I'll just start listing all bands I know.
Candidates, in alphabetical order:
Angra - Rebirth. The album open with Nova Era - a ridicilously catchy powerish metal song. I think Heroes of Sand is a great ballad thingy, too. Other than that, an all-round solid album with no weak spots.
Angra - Temple of Shadows. Another Angra album. This is their proggiest album, for sure. Most songs are very good, but The Shadow Hunter stands out as one of the best songs of Angra.
Arcturus - The Sham Mirrors. There's no other album like it. Volatile, explosive, I dunno what to call it. Aggressive? Yet very calculated and with a very well-interpreted steampunk/cosmic theme to it.
Communic - Waves of Visual Decay. Fooled by the Serpent remains a favorite "heavy prog metal" song of mine. The other songs are solid.
Devin Townsend - Terria. Ocean Machine would also be a contender if it wasn't for a couple of songs and the unnecessary loud scream at the very end of the album. Terria is just as varied and unique, but more consistent in quality.
Dream Theater - Scenes from a Memory. A recent topic on this forum. I think it's one of the best concept albums ever, and a very good album in general.
Fates Warning - Awaken the Guardian. Their best Arch album.
Fates Warning - Pleasant Shade of Gray. Their best non-Arch album. Would have rated higher if not for the ring sound at the end. Like Ocean Machine I fucking hate unnecessary shit sounds like that.
Green Carnation - Light of Day, Day of Darkness. One long, almost perfect song.
Mechanical Poet - Woodland Prattlers. Like The Sham Mirrors, it interprets a very visual theme. In this case it's Grimm-like fairytales. Amazing vocalist with a million different voices, dynamic and versatile songs, good musicianship, and no non-music fluff. Natural Quaternion is one my favorite songs ever.
Opeth - Deliverance. Almost as good as Blackwater Park.
Opeth - Blackwater Park. Their best album, and the title track is their best song.
Orphaned Land - Mabool. Deserves a mention just cuz how different it is. Instrumental combinations and arrangements never heard before.
Pain of Salvation - Be. Almost didn't put it here, but the proper songs are just so very good (Imago and Iter Impius in particular). The chatter and shit-songs are obviously not good and I always wonder who wants that shit on their music albums.
Queensrÿche - Operation: Mindcrime. Just very, very good. Quite a few 'radio' songs though.
Savatage - Poets and Madmen. Not sure if considered prog, but it's their best album. Man in the Mirror should be a metal classic, and is the ultimate whisky song.
Shadow Gallery - Digital Ghosts. Barker was a great vocalist, but this is Shadow Gallery's best album.
Sieges Even - The Art of Navigating by the Stars. Wonderful. Not many albums like this.
Symphony X - V. The initial reason why I'm here on this forum.
Current Top 5, as of September 2013.