One of the more typical questions I see come up in the various Google Help forum threads is about sites that get hacked. It is always the same thing...
A webmaster or site owner feels violated and embarrassed. At first, they think Google got it all wrong. Then they seek answers to see how they were compromised. Often Googlers and friendly webmasters explain where the hack is, how to remove it and then how to remove the hacked/malware label in Google.
But typically, this takes a lot of hand-holding between the webmaster and Google.
Google has created an outstanding hacked site resource aimed at both technically and emotionally helping the hack victim recover.
There is an 8 step walk through, designed by Google, to help webmasters in this situation. It really looks like Google put a ton of time and resources into this and we should be thankful.
The steps include:
(1) Watch the overview
(2) Contact your hoster and build a support team
(3) Quarantine your site
(4) Touch base with Webmaster Tools
(5) Assess the damage (hacked with spam) or Assess the damage (hacked with malware)
(6) Identify the vulnerability
(7) Clean and maintain your site
(8) Request a review
Clearly, this is the first place you should go if you have questions about a site of yours being hacked.
Awesome resource Google!