Here's a few great bands from the metal end of the spectrum of prog
Unexpect - http://listen.grooveshark.com/#/search?q=Unexpect%20In%20A%20Flesh%20Aquarium%20Chromatic%20Chimera
This isn't the weirdest album I have ever listened to, but it is very intricate, every instrument is given a distinct voice, and there are more instruments then one would normally expect here, but hey I guess that's why the band is called Unexpect. They even have 3, count them, 3 vocalists, and have a habit of finishing each others sentences in the songs. My favorite album of theirs is In A Flesh Aquarium. These guys are more avant-garde than prog.
Protest the Hero - http://listen.grooveshark.com/#/search?q=Protest%20the%20hero%20fortress
These guys are absolutely amazing, however I don't care much for their vocals style, just seems like it disrupts the flow of the music, feels like it doesn't belong, eh whatever, your call. I usually stick to the instrumental versions of their songs, and let me tell you they are tight instrumentally, I don't think there is a moment on the Fortress album where I have ever been bored.
Into Eternity - http://listen.grooveshark.com/#/search?q=into%20eternity%20beginning%20of%20the%20end
A bit more straightforward in nature than the other bands mentioned here, but nonetheless packing a hefty punch with all their catchy riffs, is Into Eternity, particularly their Buried in Oblivion album. This was actually the first prog-metal band I ever listened to, so I guess you could say I have a special place in my heart for them.
Kalisia - http://listen.grooveshark.com/#/search?q=kalisia%20tower%20of%20vanities
This song hails from the 2nd disc of their album Cybion, the first disc being a several hour long concept album that tells a cohesive sci-fi story, while the 2nd disc is a collection of singles performed by the band, some original, some covers of other bands such as Cynic. The track linked is one of the originals from that disc, the band employs mainly harsh vocals with a little bit of clean vocals here and there. That being said these guys sure can write a great song.
Watchtower - http://www.myspace.com/officialwatchtower
Pure thrash prog goodness, these guys reunited recently and recorded a new single The Size of Matter, and had planned to write a album titled Mathematics, however their vocalist left a year ago or so, and they still haven't made any public notice that they have found a new one, or even gave any indication that they are still looking for one, so unfortunately their career is probably over. This was one of the progressive thrash metals back from the early 90s that, like the others, just didn't seem to catch on to a substantial fanbase.
Vektor - http://listen.grooveshark.com/#/search?q=vektor%20oblivion
Yet another progressive thrash metal band, these guys aren't from the old 90s era though, they are a more recent upstart, formed in 2002. Their Black Future album is quite the sonic assault, as any thrash metal album should rightly be. They have a stated desire to create sounds with their instruments that sound otherworldly, which they succeed at in certain instrumental sections of their songs and certainly with their rather unorthodox shrieked vocals.
Well that's about it I suppose, surprised I didn't hit a word cap or something, hah. Thumbs up to Sky Architect's album mentioned earlier in this thread, listened to that a while back, it was enjoyable.