My general indifference to the blandess of neo-prog is perhaps not best suited for this thread. What I've heard from Spock's Beard, considered in some circles to the premiere act of this genre, is derivative and too pop-based. Some merits, but not enough to warrant repeated listenings.
Prog-metal is even more difficult, since many of the bands are almost aggressively anti-prog in nature. Dream Theater is one of the better bands, but their rabid fanbase turns me off to any public praise. Symphony X is slighlty better, although they're also a bit repetative.
The top three, in my mind, are The Mars Volta, Pain of Salvation, and Porcupine Tree. All three of them have illustrated, at least some point in their careers, that they are capable of creating something unique and memorable.