Google have been really helping webmaster coming up with great way to help spot if your website has been hacked.
One great method is to use the Google Alerting system set to monitor your domain against specific keywords you do not want to be associated with. If your site starts becoming associating with unrelated queries that are popular with spammers, for example keywords related to pharmaceuticals, payday loans or fake replica goods then you need to be aware as soon as this happens.