jimbeetle - 3:31 pm on Jan 10, 2013 (gmt 0)
You would be right. We added a tool to the site that let the reader search various RSS feeds and display the results on our site. To that we added a myriad of refining / filtering options, inadvertently ensuring any single term could create a mountain of pages. We then stuck a bow on the whole shebang by adding links to the various search result URLs throughout our site (by way of popular and trending lists).
Wow, well at least you know the cause of the problem. Unfortunately, it's probably going to take Google some time to untangle the mess. Best, but drastic, option might be a complete restart on a different domain.