Google has several Malware diagnostic tools in their Webmaster Tools area, but the tool has been recently updated to include many more features.  If your site has a Malware problem, Google may show a warning message in the search results indicating that the site is potentially harmful.  This is a sure signal to Webmasters to remove dangerous content immediately and, if necessary, fix any vulnerabilities on the server.  This article goes into great detail outlining how to use the tools, providing a step-by-step approach and plenty of examples.