klark0 - 11:42 pm on Oct 3, 2012 (gmt 0)
From what I've seen, it's the entire domain. In my two cases, the links with over-optimized anchor text were pointed to the homepage. Pages don't appear where they should. In queries it doesn't even rank after completely unrelated results.
It's almost like a barrier that deliberately prevents content from the site from appearing in results.
Another symptom ...New content does not rank as it should. For example, on one site a 2000 word post was published today and is indexed, but the tweet announcing it, a feed reader, a google+ post, and 2-3 snippet scrapers all outrank it for very non-competitive terms. In fact, its not even in the Top 100.