crobb305 - 10:33 pm on Mar 18, 2011 (gmt 0)
I see the same thing also, a few pages moved up, but most moved down. It seems the net effect was to bring my whole site down 50% to 60%. One page that moved up, and still ranks on page 1 for some good terms, is a "thin" affiliate page. It was a page that I linked to most conservatively (only once from the homepage, and in the top navigation of all other pages). Pages that got hit the hardest had 2 or more affiliate links AND were linked most frequently (3+ times) from the homepage with varying anchor text.
I did have one page that suffered the greatest position drop (-300 according to WMT), and that page had a spelling error in the top header tag <H3> and a very short/duplicate title/desc. Since making those corrections, WMT reports a gain of 200 positions for that page.
Most of my pages are error-free, ad-free, informative, and unduplicated. Only 4% of my pages contain any affiliate links whatsoever. So, I am pretty much at a loss. I have revamped some of my content on the thinnest pages (that contain affiliate links), and will eventually file a reincl. request if these changes don't help.