Prog is my cup of tea. Most of the good ones have already been mentioned but a couple of my favorites have been left out. Namely:

Ayreon - The Human Equation
http://www.youtube.com/watch?v=TFfKWaM1Bp8

Ayreon - 01011001
http://www.youtube.com/watch?v=TFfKWaM1Bp8

Guilt Machine - On This Perfect Day
http://www.youtube.com/watch?v=Jn1E9aMZuKE

They may be a little cheesy but the riffs and some of the guests are just immense.

I also recommend:

Devin Townsend - Ziltoid the Omniscient
http://www.youtube.com/watch?v=FlBGIx3qbiM

And any Mastodon and Baroness album.

Also, this is one of the most amazing EPs I've ever heard and it's pay-what-you-want:

David Maxim Micic - Bilo 1.0
http://davidmaximmicic.bandcamp.com/album/bilo-10-ep

I liked Bilo 2.0 more personally, my favourite EP of all time is Hail the Sun - Elephantitis, it's progressive post hardcore/mathrock, really cool stuff.

Here's the first song off that EP
http://www.youtube.com/watch?v=N3sPHdTYqmw

Jackpot! Going to have a lot of music to look into this weekend.

Portugal. the Man - In the Mountain in the Skies, Censored Colors

http://youtu.be/ldmoHDQ9Adw

Anything by The Decemberists is amazing.

The Antlers - Hospice