Tell us about the site. A while back, Google delisted all of a certain type of TGP script, presumably as a test. A week later, all the sites returned.
You may have existing link trades with sites that may now be deemed "bad neighborhood" sites. Check your outbound links for sketchy sites that Google may have issues with. Remove those links.
Any chance of a site hack? Check your .htaccess file and robots.txt.
What's the niche? Do you have user-generated content? Check that stuff for spam.
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