Updated at 4:45pm Google's Matt Cutts posted on Google+ that the reason so many people are seeing these notifications is because they decided to also send them out when a penalty will NOT follow. Google is notifying webmasters of unnatural links pointing to their site even if the links will not hurt them. Shouldn't Google's message be clear about that distinction? Yes, but it is not and thus webmasters and SEOs are a bit concerned.
Here is what he wrote:
If you received a message yesterday about unnatural links to your site, don't panic. In the past, these messages were sent when we took action on a site as a whole. Yesterday, we took another step towards more transparency and began sending messages when we distrust some individual links to a site. While it's possible for this to indicate potential spammy activity by the site, it can also have innocent reasons. For example, we may take this kind of targeted action to distrust hacked links pointing to an innocent site. The innocent site will get the message as we move towards more transparency, but it's not necessarily something that you automatically need to worry about.
If we've taken more severe action on your site, you'll likely notice a drop in search traffic, which you can see in the "Search queries" feature Webmaster Tools for example. As always, if you believe you have been affected by a manual spam action and your site no longer violates the Webmaster Guidelines, go ahead and file a reconsideration request. It'll take some time for us to process the request, but you will receive a followup message confirming when we've processed it.
My big issue with this is that Google told us these manual messages are penalties and now they are no longer penalties. It is confusing in so many ways for webmasters.
Here is the remainder of the story I wrote this morning:
In July 2011, just about a year ago, Google first started sending out notifications of unnatural links pointing to your web site. Then in March of this year, Google ramped up this notifications and tons of webmasters received them.
It has been pretty quiet recently on this front, with only a few complaints per day in the forums about these notifications. But that all changed yesterday when tons of webmasters began receiving these notifications.
Almost all of them plead innocence but the fact of the matter is, they received this notification and they most likely will see a downgrade in ranking within the week. This is a manual penalty that likely lasts 6 months or so and requires a reconsideration request to be removed before the penalty expiration window. Note, if you do nothing, the penalty will probably happen again.
Did you get a notification in the past day or so?