StopBadware and Commtouch have published an interesting report on compromised websites. The report talks about how website owners have been hacked and repair damage and presents interesting statistics on the subject.
The study found that, in most cases, legitimate websites are compromised without the website owner even noticing that their website has been compromised. Over 90% did not notice any strange activity, although their websites were misused to redirect visitors to other links, send spam, host phishing sites or distribute malware. Over 66% did not know how the piracy occurred.