GWT is going to start notifying you in your GWT account if they believe your site or sites have malware installed. They'll also offer a process where you can request a review and get the notice removed, which has been a big bone of contention from what I understand.
If you find that your site is affected by malware, either through malware-labeled search results or in the summary for your site in Webmaster Tools, we've streamlined the process to review your site and return it malware-label-free in our search results:
1. View a sample of the dangerous URLs on your site in Webmaster Tools. 2. Make any necessary changes to your site according to StopBadware.org's Security tips. 3. New: Request a malware review from Google and we'll evaluate your site. 4. New: Check the status of your review. * If we feel the site is still harmful, we'll provide an updated list of remaining dangerous URLs * If we've determined the site to be clean, you can expect removal of malware messages in the near future (usually within 24 hours).
[edited by: tedster at 5:37 pm (utc) on Aug. 14, 2007] [edit reason] added the link [/edit]