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UPDATE: Microsoft CEO Still Sees Possible Yahoo Deal (March 19, 2009)
I have a large site that does well in Google rankings, but it's under a penalty in Yahoo. Yahoo has indexed only one page out of over 2,000 pages, even though the site is also in the Yahoo directory (edited by humans). I get no traffic from Yahoo SERPs, even though I get hundreds of visitors via Yahoo answers links (posted by humans). [Memo to engineers: try to resolve the contradiction.]
I have another site that is similar in structure and Yahoo loves it. Gets great SERPs, lots of Yahoo traffic, and has every page on the entire site indexed. I have no idea why Yahoo loves one and hates the other.
In any case, I'd like to see if a Yahoo SEO firm could get the penalty lifted. But in recent news there's talk about Microsoft buying Yahoo Search. I currently do reasonably well with MSN SERPs. Presumably if MSN buys it, and revamps Yahoo Search, or replaces it with its own algo, any time and money spent trying to figure out Yahoo's current algo would be wasted.
What would you do? Do you think Microsoft will buy Yahoo Search? And if it does, do you think the sorry Yahoo algo will be killed with a violent death? :/
As for Microsoft buying Yahoo, I don't really see it happening, nor do I really want to see it happening. If it does, however, it would be very foolish of Microsoft to rid of the Yahoo algorithm altogether. If only they'd do something about their communication with webmasters - I suspect their algorithm may be too vulnerable for that.
Sites can have a Yahoo directory listing and be listed in Yahoo news search results and still go missing from the main search engine results.
Is there a lot of cross linking going on with your site? Yahoo can clampdown heavily on this.