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trakkerguy - 1:40 am on Feb 3, 2007 (gmt 0)
A site I had previously consulted on and keep tabs on was hit in December and has been fluctuating, but mostly down since then. This site has 4 subdomains with URLs like "bluewidgets.domain", "redwidgets.domain", "greenwidgets.domain", and "yellowwidgets.domain". The index pages are very similar, but optimized for keyword search to match the subdomain name. The index pages for these subdomains ranked from #4-30 prior to December. Now on a search for "blue widgets", the domain.bluewidgets index page is buried deep in serps. All the other subdomain index pages rank much higher than the bluewidgets.domain index page. In fact, every page on the site ranks higher for the terms than the index page that is most optimized and used to work best for those search terms. Even more interesting, is that the bluewidgets.domain index page isn't "penalized" for every term, just for a search on "blue widgets". If you search for "green widgets", the bluewidgets.domain index page, and every other page on the site, will rank higher than the greenwidgets.domain index page. All the pages on the site follow this pattern. A page will rank ok for some search terms, but terms they are most optimized for are buried in the serps. Notice how many posts here refer to losing rankings for selected keyword searches, even though they've done nothing wrong? Yet other keyword searches will still find the "missing pages".
It's probably multiple "filters" being tweaked continuosly, but a big factor, IMO, is definately a change in how much keyword optimization is allowed before you have problems.