PPC_Chris - 5:58 pm on Jun 9, 2011 (gmt 0)
Here is my take from the whole situation...
I think that Panda penalizes sites (or portions of sites) that hit a certain threshold of what Google considers low quality signals (thin content, too many ads, possibly scraped content, etc.).
Panda 1.0 penalized a lot of sites. Panda 2.0 and 2.1 expanded the threshold and more sites were hit with the penalty. Sites have not recovered from the Panda penalty. Panda is not running on the fly, so even if webmasters have taken action to fix the site, the penalty will not be lifted immediately but only if/when Google decides to re-calculate the penalized sites.
I believe the penalty is a %, in that Google discounts your site (or a portion of your site) by a %. In other words, all your pages now have x% of the value that they would have w/o the penalty. This differs from a -50 or -20 penalty. This explains how sites can still have the top few listings for brand-specific terms while losing rankings for more competitive terms. I have not heard of a drop in indexed pages or a sitewide de-listing due to Panda. Low quality content on certain pages of your site can cause your site to hit the Panda penalty threshold, and the rest of your site can get penalized, dropping rankings for pages that have no issues with low-quality/thin content.
I don't see how Panda can't be seen as a penalty. If it was just an algorithm change, there would be webmasters would be reporting minor loss of rankings. The rankings change would look like a bell curve - with almost all websites being affected in at least minor way. Instead, it seems pretty obvious that your site either got smacked down by Panda or didn't. Plus, many sites actually improved rankings after 1.0 only to get decimated by 2.0 or 2.1.
What I am hoping for is that at some point (SOON!) Google will re-run this algorithm and re-calculate sites that have hit this threshold and penalties will be lifted for those of us who have correctly identified and fixed the issues Google saw with our sites.