Of your list, Linda, I've heard/have The Incident, Black Clouds and Silver Linings, Frequency, and Horehound.
The Dead Weather/Horehound - I'll go ahead and address this one - I really enjoy it (ducks and runs) . . . guess there's just something for everyone in this world - there's a lot of sexual tension in their music which I find intriguing.
The Incident - PT is one of those bands that there IS no BAD music from, at least, I haven't heard it yet. I enjoy all of their catalog. And this is certainly one of the strongest albums of 2009, but ranked among all of PT's catalog, I'd have to place it somewhere in the middle, I think. There seem to be those people who really enjoy their "middle period" with it's spacier tone, and then those people who really enjoy their later things with the harder edge, and I'm definitely one of those. Deadwing so far is my favorite PT album, and I'm always hoping for more along those lines . . .
Black Clouds and Silver Linings - I like this one better than their previous, Systematic Chaos, overall. The Count of Tuscany is worth the whole album, and I'd love to hear it LIVE! I also really like A Nightmare to Remember and A Rite of Passage. The Shattered Fortress is a good culmination to the "12-step saga" - looking forward to hearing all of those played as a suite in concert. Not my favorite DT album, but not the least favorite either - a worthy addition to their catalog.
Frequency - wonderful music with a "Yessy" feel to it - I've enjoyed it a lot, and hope to extend my IQ catalog in the near future.
There's a few others on your list I would probably enjoy hearing as well.
As far as my personal list goes, I would definitely put in a vote for Transatlantic/The Whirlwind - I'm really enjoying that one!
Two other of my favorite performers also had new releases this year. Adrian Belew's "e", with his "Power Trio", is full of those things he does so well . . . lots of Crimsonesque feel to it as well. And Super Furry Animals released Dark Days Light Years - very cool music which I like a bit better than their previous release Hey Venus, although I haven't found anything they do that I DISlike . . .
Not prog - but another one I've enjoyed this year is Franz Ferdinand/Tonight - my son turned me on to them - good strong pop with a lot of 60's influence.