It is difficult to tell, as I the cpanel doesn't allow me to view all of my logs since the inception of the site.
My guess is that it was a custom login script that I wrote.
They chmod'd a number of files which turned out to be the real nightmare in the whole ordeal. It wasn't that difficult to delete the php scripts they had uploaded.
As Annie said, they were "redirect" scripts for spammers, encoded with base64, pointing to mostly russian domains.
If anyone is looking for a good (and safe) decoder for base 64, I found this one to be useful:
http://www.opinionatedgeek.com/dotnet/tools/Base64Decode/
Regards,
The Captain