Back in September 2005, Google began emailing webmasters about violations to the Google webmaster guidelines. Then in March 2006, Google started stepping up those notifications. Webmasters were loving Google reaching out to them with issues, so they can address them quickly.
But then the spammers and hackers got involved. In May 2007, we reported that fake Google emails were being sent to webmasters, scaring them. These emails repeatedly went out and Google had to do something.
In July 2007, Google stopped sending email notifications and created a message center in Webmaster Tools to securely notify webmasters of issues. The only problem is that these webmasters had to have a Google Webmasters Tools account and verify their sites, to see these notifications. But I guess it was better then the issue with having fake emails go out.
I believe, but I am not 100%, Matt Cutts of Google asked in one of the panels at SMX West, just a month or two ago, if we want emails again. Most people said yes. But validating the email came from Google is hard.
Today, I see a WebmasterWorld thread that notes someone received an email from Google, notifying his site was hacked and thus delisted from Google until the hack is removed. The email says that he should login to Webmaster Tools, validate his site and confirm these details. Then remove the hack and clean up the site, and then submit a reconsideration request. In addition, the email gave specific details on how his site was hacked and what mess the hack left on his site.
So it appears that Google may be emailing webmasters again, to notify them of hacks and other issues that Google may find quicker then some webmasters.
Forum discussion at WebmasterWorld.
Update: A Google Webmaster Help thread has a copy of one of these emails.