From my past experiences, I know that many legitimate and honest webmasters have been banned from Adsense, because of invalid clicks. The only reason they were emailed by adsense- "Invalid clicks."

It can be very simple. The webmaster messes up with someone at a forum and the other person thinks of teaching a lesson. He find out his sites and starts click bombing until Google bans the site.

There are some precautions to take though. For example, it is a good idea to use scripts that prevent the same user from clicking on an ad more than once. The ads may also be rotated using ad servers like OpenAds.

However, IMO, thinks will change. Adsense is shifting from pay per click to pay per action model. Of course! Adsense Referrals is still in beta. When the switch is complete, we will get complete immunity like with clickbank and commission junction.