i had a bit of a traffic drop recently because of this panda thing, and my number of indexed pages has halved. But after digging around in my stats and WMT, i noticed that google has been crawling a load of non-existant pages.
im talking about pages which existed on my site at least 12 months ago, which i deleted, and have never shown up as errors in WMT before. now all of a sudden they are back and i've got bazillions of 404 errors.
WMT shows you were it got the URL from, and some of them are external sites. If i follow these URLs then more often than not the link does not appear, so im guessing google has crawled on old version of that page too, and the link has since disappeared.
so i'm thinking that might be part of the reason for our traffic drop.
google has crawled a very old index for panda, and is doing the same for all the other sites, so all our backlinks will be screwy, and all our internal links too, and all our new pages have yet to be indexed.
...even if your site has been thoroughly indexed, you might want to site it out before making changes, so google can factor in all the other sites too.