A few sites I'm associate with have been infected with malware. It appears as if one of the site owner's FTP application was infected and all affiliated sites were infected with the same malware.
I was directed to blog.unmaskparasites.com and it seems to have a tremendous amount of information on just this problem.
From Hidden Iframes to Obfuscated Scripts
10 FTP Clients Malware Steals Credentials From