I'm seeing a ton of pages showing up as supplemental results in Google, but when I click on them they show up as error pages. It may take months, but Google will eventually spit them out of their index if you have your custom 404 page set up correctly.
Some of these supplemental pages were Amazon affiliate pages. Google and Yahoo both HATE these affiliate networks and they can cause major ranking problems for a web site. It was a good idea that you removed them.
The search engines are trying to get rid of the web clutter by not indexing all of the affiliate / made for Adsense type sites. With those thousands of Amazon affiliate pages your site may have been classified as a "bad neighborhood".
Have you lost any SE rankings in Yahoo or Google?
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