So far, it appears that some of Yahoo's recent change involves the way they handle links. In particular, it looks like they are discounting links that they feel are part of link networks or affiliate programs.
One of our sites dropped in Yahoo, and their response suggested that the site in question was part of an affiliate program (it's not).
What we have done is move almost all of our outbound links to a sub domain of the web site (since SE's currently treat sub domains as unique domains and not part of the root domain).
By taking this approach, any time a search engine questions our outbound links the root domain will not be penalized.
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