Best for me was easily Pearl Jam's self titled. Of course, it's a bit of a bias, but it was their best effort since Vs. (which is saying a lot in my mind). There were only two songs on the CD that didn't work for me (Parachutes and Wasted Reprise) and even then I can listen to those two if I'm in the right mood. Not sure what did it but they just seemed inspired and it led to something great.
Honorable Mention: Revelations by Audioslave and Wolfmother by Wolfmother (Came out in the US in 06)
I think my most disappointing album was Tool's 10,000 Days. I'm not sure what I was expecting, but after such a long wait...I just expected a bit more. I did kind of see it coming after APC put out Emotive, which was their worst album by far. I don't want to blame it on Maynard, because I know that the band as a whole put's a lot into the song writing, but when both of the bands he's in manage to put out their worst albums, I can't help but think he has something to do with it.
Dishonorable Mention: Decemberunderground by AFI
What has been your favorite album of 2006?