Two link farms link to a mass of non-existing threads on site. It seems like Google bowling. I found this in my Google webmaster tools. Is there any way that I can make Google aware of the issue or counter this?
I don't think that Google would do anything, as it is not their problem. The good news is that Google bowling doesn't work any more (if it ever really worked) and that G knows that you have no control over what other sites link to on your site. If you are getting traffic on those links and want it to stop, you can create a custom 404 page so that all traffic going to pages not found are routed to your custom page. Then, on the custom page, use a scripting language to get the referrer. If the referrer is one of these forums send them to a page with almost nothing on it, maybe just a message that you feel the forum is trying to hurt your site. The big thing is never, never, in any way link back to these forums. If you do, it will look to Google as though you purchased the links to your site.