TheMadScientist, I think I mentioned to you an observation a month or so ago, and you may be seeing the same thing:
In my sector, many of the established sites (5 to 10 years old) that have been penalized tended to have a sitewide navigation that linked to "money" pages using keyword anchors. This structure is highly effective for funneling traffic and increasing conversion rates, but I feel that Google is spanking it. Now, the sites that rank well do not have this structure. In fact, some of them have very poor navigation, perhaps linking to only one or two internal pages from the homepage, or only to administrative pages such as "FAQ", "Contact", etc.