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I dont think its a penalty, its just inktomi that does a bad spidering and pure servers so they loose some sites.
As mentioned in the other posts, all I can find is the home page.
What types of sites are you guys running just to rule out the possibilities?
Mine is for some highly competitive KWs and is a large database driven site with lots of mod rewrite stuff to change the urls to more friendly looking .htm pages.
The only other factor I can think of is a large amount of crosslinking with related (but not overlapping sites) I run.
I do think it is a filter as my category pages have disappeared but my home page still ranks (around 90-100) on the terms but below lots of other sites with low relevance.
It isn't that the pages have been dropped form the Yahoo index as I can find them if I hit "similar Pages"
Wierd!