If it was something like that, we have no control on controlling that.
Sure you do, you remove shady ad networks from your site and find something more reputable.
I would look at all included files, the home page, check your DIRECTORIES, make sure you don't have a hacker in your site that added a new folder on your server. You may be serving up malware from a path you're not even familiar with from your own box, including a possible subdomain.
If any part of your site has an issue, they red flag the whole site.
One way to find this stuff using Firefox is to install something like NoScript, and then use their tools which show you all of the scripts attempting to load from your site. If there's anything you're not familiar with, it's probably where it's coming from. I've used NoScript to diagnose a couple of sites with malware before, not mine of course ;)
Hope that helps.
P.S. FYI, If you use a 302 redirect script to track all outbound link clicks, Google will actually attribute the malware to the page ON YOUR SITE that contains the redirected link! Damned annoying and very misleading.