I have just received a malware notification from Google today, claiming that my site has suspicious content and they will put a warning in their search result. I checked the Stopbadware guidelines but could not find any problem with my site. A Google diagnosis also confirmed that there was no suspicious content or malicious software hosted in my site over the past 90 days. The only problem is my site is hosted in a network of >40000 sites and some of them have suspicious content that can download malware to the visitors' computers. My site is hosted in a shared server so I can't control the content of the other sites (and these sites may or may not know they serve suspicious content themselves). I wonder if the more experienced webmasters can suggest ways to tackle this problem. I have already contacted my hosting company and asked Google for a site review and explained the situation.
Check your server logs for suspicious activity on your site. Check your code to make sure you haven't allowed a widget of some kind permission to execute code (I see this on wordpress sites that allow php execution inside articles but forget that widgets in the sidebar can execute it too).
If the problem is not on your site talk to your host, they can most readily find the problem site on your shared server and remove it. File a complaint if you have to, your service is being affected.