For some reason, I was under the impression that there was one manual action that Google sends out to some webmasters that is a warning of something that looks spammy but no negative manual action was taken on the site.
I was wrong.
Former Googler, who worked in the manual actions team, Kaspar Szymanski, posted on Google+ that any web spam related manual action always impacts part of all of the site in a negative way.
To be absolutely clear: some WMT messages can be just warnings as for instance you've got a ton of 404's my friend, everything ok with your site?. These are generally technical escalations. However when it comes to web spam related messages, they specify that some manual action (not an algorithmic recalculation) has been taken, all of them. The impact of that manual action can be imminent or not, that depends on a number of factors though.
I tried to look back at an example of a manual action notification that I thought did not impact the site, but maybe it had to do the the granular penalties we've seen?
It is very important to take such warnings seriously. They are not sent likely and should be considered a wake up call. If received first thing to do is to take a long, hard look at the site's backlink profile and compare it against Google Webmaster Guidelines.
Please don't ignore Webmaster Tools Messages!
Forum discussion at Google+.