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tedster - 3:13 am on Dec 1, 2008 (gmt 0)
Maybe it's that word "penalty" that's getting in the way. I don't think there's a penalty against the domain here, just a removal from the top of the SERPs for enough time to be sure the site is accessible again. Google is only paying attention to their own users, and that's their core purpose.
I often agree with a lot of what you say, but on this we see things differently. To me it makes plenty of sense for Google not to show links high in the search results if the site's server isn't responding. Why wouldn't Google protect their own user experience that way?