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I asked a knowledgeable member here what he thought, and he said that Yahoo probably "cloaks" the page for spiders, giving the spider clean URLs, but keeping the indirect tracking URLs for all other visitors, so clicks can be tracked. I thought that was quite logical, but when I looked at the directory using SIMSPIDER, the links were the same.
Any further thoughts?
A quick check of the Google cache of a Yahoo directory cat shows they don't cloak.
I don't see how they can pass PR, unless Google has programmed the spider specifically to decode the indirect Yahoo Directory URLs. These URLs would not pass PR or be crawled if found on another site.
Yahoo uses 302 redirects to their indirect links to the destination website. Googlebot simply sees the URL in the directory then attempts to follow it. It then sees that it is a redirect and then treats it as if it were a direct link to the site.