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.Update
: Thanks to everyone who gave feedback on this change. An engineer worked over the weekend based on the suggestions here, and starting on Sunday we made two changes so you can tell the "individual links aren't trusted" messages from the "our opinion of your entire site is affected" messages.
First off, we changed the messages themselves that we'll send out to make it clear that for a specific incident "we are taking very targeted action on the unnatural links instead of your site as a whole." So anyone that gets a message going forward can tell what type of action has occurred.
The second change is that these messages won't show the yellow caution sign in our webmaster console at http://google.com/webmasters/
like our other webspam notifications. This reflects the fact that these actions are much more targeted and don't always require action by the site owner.
Thanks again for the feedback, and we'll continue to work on ways to provide more useful and actionable information for site owners.