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.

From the notification on the Webmaster Central Blog [googlewebmastercentral.blogspot.com]:

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]