A client of mine was hit hard by Penguin, from 80,000 visitors per day to 40,000. On the surface, nothing made sense. They don't and won't buy links. While looking at their BL profile, only -1,000 questionable links were established, all from junk spammy websites, but that didn't come close to the hundreds of thousands of genuine links they actually had from everything from personal blogs to tabloids inc BBC News, CNN etc.
This is an established website, since 1996 and an authority in it's niche. Nothing made sense.
During a recent upgrade to their message boards, I found that whoever performed the last upgrade (pre penguin), created a double 301 redirect from all old urls, to all new urls to accomodate a change in url structure.
As you know, Google only follows 1 redirect and then gives up, meaning that none of the link juice from the past 10 years was being counted. Suddenly it made sense why despite their seemingly perfect link profile, they were hit by Penguin.
 My theory is/was, the link juice lost from the double redirect, was causing the ratio of spammy to good links to rise. The bad links were all pointing to the main website, therefore not effected by this issue. And the majority of good links, were pointing to threads in the forum, all of which were effected.
Anyway, I just wanted to post this up, as it's something that literally didn't cross my mind to check and while asking for advice from friends in the field, none of them suggested it either.
I resolved the issue about a month ago and now waiting for a refresh.
[edited by: realmaverick at 5:18 pm (utc) on Feb 26, 2013]