If you've been hit by Penguin 2.0 (or 1.0), you must heavily analyze your link profile and identify unnatural links to remove. For some sites, this is a daunting task. There are a number of sites I've analyzed that have hundreds of thousands of links to remove (or more). And the more links you need to remove, the harder it is to keep track of your progress.
Read more at http://techwy.se/KGmiX