Qualys' paid service is called Go Secure, and for $995 a year, it provides additional protection. For instance, it checks to see if your web certificate is up to date, along with other vulnerability scans. Additionally, if a site subscribes and is deemed safe, it is given a security seal to comfort visitors. Once infected, though, the seal is yanked from your site and isn't returned until Go Secure determines everything is OK.
Both services are in beta and available today.