Pollock
Local Buffalo band. I'm friends with the guys. I'm not trying to promote their stuff (although it goes hand in hand); they really love prog rock like Tool and sound kind of similar. The first song on their myspace is live, and so the vocals are difficult to make out; but the other songs are studio recordings.
http://www.myspace.com/wnypollock
As far as other popular bands go:
A Perfect Circle (you probably already know them)
The Tea Party (Canadian prog rock w/ eastern influences)
I love this genre, but more so old progressive rock (Floyd, Genesis, Tull, etc.). But there are some great modern prog bands. I really love The Tea Party, but unfortunately they're not around anymore. They have a really unique, interesting sound. The lead singer/guitar player (Jeff Martin) is a genius.