goodroi - 3:49 pm on Oct 31, 2011 (gmt 0)
Not all penalties or filters are reported in Google Webmaster Tools.
Let's start with the basics:
Have you checked your log file to see if Googlebot is regularly crawling your site?
Have you tried to retrieve your site as Googlebot to make sure there is no issue?
Have you checked your page headers to make sure no one added anything to them?
Have you checked your robots.txt file & htaccees file?
Have you checked your backlinks to make sure there is no change? Drop in good links or increase in spammy links?