I had this happen on a site I manage.
Use the Google Webmaster Tools that StopBadware lists. When you go through the process of activating through the GWT, it should show you where the problem cropped up. On my site, one time, it was that the host had been hacked and code injected into all the index files. Another time, it was a .js file that had code injected into it.
However, it's also possible, as mentioned, that it is ads causing the problem. See what the GWT specifies, that should help clear it up. Then once you've found the source and cleaned it, request a new review - takes about 24-48 hours.