This Yahoo SiteExplorer suggestion needs some votes. It basically suggests adding an option to just show 1 link from each domain. I commented below that it would make sense to add in the results somewhere "and 1,000 other links from this domain", but I agree that being able to filter out all the sitewides would be very nice. So people, if you agree, please vote on it!
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Yahoo SiteExplorer suggestion
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I have to agree with you. I was facing the same issue this weekend.
Can't say Yahoo is doing too bad: the new 'Delete URL' (including subdirectories / files) has been quite nicely integrated. A much better job than Google does, at that point.
They're improving rapidly, yeah.