I'll second the Archetype, Eternity X (The Edge is great, others are ok), and Sieges Even (only the last 2 "Uneven" and "Sophisticated"), those are the best bets for what you're looking for.
The first Ice Age disc is also great, but the 2nd one was pretty weak.
Zero Hour and Spiral Architect are amazing, but I do believe you have heard them both, and they're more in the tech arena than prog.
Gracepoint is great, but not so progressive, IMO.
Ayreon's "Flight of the Migrator" and Star One "Space Metal" are both good, but pretty cheesy at times.
Pain of Salvation, Ark, and Soul Cages are on the lighter side, thus they never kept my interest long.
And Depressive Age are great, but not really prog, more thrash/doom, kind of like Abstrakt Algebra, but less doomy. The later stuff, especially Electric Scum, could be considered prog; it's pretty eclectic.
Ion Vein is really power metal, but it's pretty good.
Others not mentioned:
All That I Bleed - IMO what Dream Theater should sound like, and I really like Dream Theater
Dimension - singer's kind of weak, but music's pretty good
Power of Omens - 'course you already heard them, I don't like the singer much either
I'm on an instrumental kick again lately, got any recommendations? Some more stuff like Happy Family or Doctor Nerve would be great.