Here is how I found it:
On one website(~500pages) with over of 300 pages indexed in Google, I've used an Iframe linking to other sub-domain in order to display a relevant content.
When I removed the iframe almost immediately, in less than 24 hours my indexed results came up from 300 to 360.
I started searching on the forums and it appeared that Google penalty filter was triggered by such a huge usage of iframes(mistakenly taken as poisoing attack).
Here is short text from Matt Cutts on this:
"Essentially, our search algorithm saw a large area on the blog that was due to an IFRAME included from another site and that looked spammy to our automatic classifier."
Remove all the iframes that you have and replpace them with ajax calls or just static HTML content.
Wait a few days and run: site:http://yourwebsite.com to see the difference in the results!
Good luck! by Nevyan Neykov