Dozens of general, non-topical directories were penalized recently due to behavior Google considers manipulative. The issues seemed to stem around allowing anyone on any page with deep linking and uncontrolled anchor text.

Directories requiring reciprocal links are not conducive to natural link building campaigns. That seems to be a large contributing factor along with many of the directories advertising on sites and forums that do seo and attract webmasters of all sorts.

These directories penalties did not include a loss of PageRank, at least not yet. The directories are generally still indexed but don't rank for anything other than their tld. It would be more appropriate to say that certain pages are listed, while others have been removed from the index.

Some of the directories impacted include Aviva, Alive, Elegant, ewebpages, and Haabaa.

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