Wow, lots of great recommendations.
Some specific albums to check out:
Andromeda's Extension of the Wish - one of my favorite progressive metal releases ever. Any fan of Dream Theater should own this. Lots of Petrucci-esque riffs coming from Johan and lots of cool instrumental passages. And they're from Sweden, so you can't go wrong.
Power of Omens' Eyes of the Oracle - some great technical prog. Fans of Geoff Tate should take note. Highly recommend their 20-min epic Test of Wills.
Adagio's Underworld - also one of my favorite progressive metal releases ever. A must own for Symphony X fans. The whole band has got some good chops, and while the singer is no Russ Allen, he's certainly not bad. I highly recommend this over Sanctus Ignis because they seem to have developed a bit more of their own sound on this one.
Wastefall's Soulrain 21 - For Pain of Salvation fans, I need to recommend these guys. They're a relatively new progressive band from Greece, and I noticed on their website they played a few shows with PoS. The singer is the closest I've heard to someone sounding like Gildenlow, especially in the mid-ranged vocals (and the rapping).
While it's obvious PoS is a huge influence for them, I wouldn't quite call them a clone. Pain of Salvation and Wastefall are as similar as Adagio and Symphony X. Similar styles, but they still have their own sound. You can listen to some clips here:
www.wastefall.com
For Zero Hour fans, check out Jasun & Troy's progressive/industrial/death metal band Death Machine. Also, check out Jasun Tipton's new jazzy solo album Seduction.