You folks picked some excellent bands (particularly Ark, Conception, Hurricane, Lemur Voice, Mayadome, and Without Warning)! I thought of a few that haven't been mentioned yet:
Altura--Quite a unique prog band. The singer had a fairly different style than most guys in this genre, and the musicians were top notch.
Auditory Imagery--"So Alive" is an underrated prog album.
Jason Becker--I know he's not a band, but he made some of the best guitar music ever. This is clearly a case of the world being robbed of a true artist.
Black Sabbath with Tony Martin--In my opinion, the best era for this band. Tony has an incredible set of pipes, and I think Iommi's playing only improved during this time.
Cairo--Take the best elements of ELP and Styx, and you have a band that I really miss.
Centaur--I don't think many people knew this German power/prog band. It's a shame, as these guys got better with each album.
Chiaroscuro--They only released one album, and I don't think people knew what to make of them at the time. They'd probably be considered brilliant now.
Clockwork--If Pain Of Salvation took more cues from the '70s, I think this is what they would have sounded like.
Conditioned Response--One of the best AOR bands to come out of the mid-90s.
Defyance--Another band that improved with each album. Come on, Lance, light a fire under their asses!
Divine Regale--Great vocal harmonies, great keyboards, and great songwriting.
Dream Child--One of the best French bands I've ever heard.
Heir Apparent--"One Small Voice" is one of the most underrated albums ever made. EVER!
Imperium--Sort of a thrashier Fates Warning, if you will.
Mercury Rising--Some of the most intelligently written prog I've ever heard.
Mystic Force--Heavy as hell with intricate musicianship. "Man Vs. Machine" was their best.
Samson with Bruce Dickinson--"Head On" was ahead of its time.
Stride--Is it too early to miss them?
Okay, I swear that's it!
Stay metal. Never rust.
Albert