A WebmasterWorld thread has a webmaster sharing a notification message he received via Google Webmaster Tool. The interesting part is that this notification is very specific that although the site has a penalty, the penalty is only being applied to a specific page or section of his site.
Google said the penalty is "very targeted action to reduce trust in the unnatural links," but not in the other links pointing to the site. Google said they took "very targeted action" because they know these "links may be outside of your control" and thus don't want to penalize you for that.
Google did add that they "recommend removing any unnatural links to your site" and when you do, you are recommended to "submit a reconsideration request."
This is the first time I've seen someone post a webmaster tools message of a penalty with this type of language.
We do know that Google does often take very targeted and granular action on sites, as to not impact the whole site or all the links. This came up recently with the BBC penalty and has come up before.
Have you seen this message?
Personally, I think this is great because the previous penalty notifications were never that specific and webmasters went overboard to remove all links pointing to their sites. Hence the disavow tool.
Forum discussion at WebmasterWorld.