mm.. I'll put recommended albums in parentheses, and my favorites of the favorites in bold.
1) Classic PR:
Genesis (Selling England by the Pound)
King Crimson (Discipline)
Ozric Tentacles (Erpland)
IQ (Dark Matter)
Marillion (Misplaced Childhood)
Frank Zappa (uhhh.. take your pick)
Pink Floyd (Wish You Were Here)
..i don't listen to much old stuff, honestly.
2) Modern PR:
Riverside (Out of Myself)
Porcupine Tree (In Absentia)
Gordian Knot (Gordian Knot)
Freak Kitchen (Move)
Bubblemath (Such Fine Particles of the Universe)
Estradasphere (Buck Fever)
The Flower Kings (Space Revolver)
The Tangent (The Music That Died Alone)
Bumblefoot (Normal)
Upsilon Acrux (LST Pirates of Upsilon)
3) Classic PM:
i'm not really sure what's supposed to go here? classic progressive metal is sort of an ambiguous term. do you mean bands that are now defunct? off the top of my head..
Cynic (Focus)
Watchtower (Control and Resistance)
Lethargy (It's Hard To Write With A Little Hand)
Atheist (Unquestionable Presence)
Clockwork (Surface Tension)
Maudlin of the Well (Bath)
4) Modern PM:
Pain of Salvation (Entropia)
Aghora (Aghora)
Behold... the Arctopus (Nano-Nucleonic Cyborg Summoning)
Coprofago (Unorthodox Creative Criteria)
Planet X (Live from Oz)
Ayreon (Into the Electric Castle)
Frantic Bleep (The Sense Apparatus)
Opeth (Blackwater Park)
Meshuggah (Chaosphere)
Linear Sphere (Reality Dysfunction)
I've lost my touch for "prog" specifically, because much of today's "prog" isn't very progressive at all. So, you may find that some of the above artists aren't in the style of stale and predictable 'prog', but instead in the world of music that is actually progressive in that it pushes the boundaries of the artists's chosen genre and/or of music. Official "genres" jump around a bit, but the general theme remains forward-thinking metal with an abundance of avantgardness, atmosphere, and futurity (i dunno if that's the right word to use? lol).. just like you wanted.
There are many missing artists, but choices were limited
edit: forgot to include one of the greatest bands ever :O