The virus that owned the old site (along with every other index.* on my webspace) was a variant of the Gumblar.cn virus http://blog.unmaskparasites.com/2009/05/07/gumblar-cn-exploit-12-facts-about-this-injected-script/

It infected my computer just by visiting a site, found my stored ftp credentials from FileZilla (teaches me not to store my passwords), logged into my webspace and proceeded to modify any index.* file. Very evil, very clever virus. Right on that tipping point between me being impressed and me being horrified.