The next time you find something like this, run stat on it and archive all your available logs for anything that has had access to the directory in question. These often come in through flaws in a web application like WordPress, Joomla, osCommerce, or jCow. A good incident response admin can often tell you how it was done and how to fix the security issue.

There's often more than one file, and sometimes they also inject malicious code into legitimate files.

For what it's worth, there are also often FTP uploads or uploads through a control panel's file manager. The attackers do that by compromising a PC and looking for passwords saved in FTP clients or web browsers. So scan and secure any PC you have, any on the same LAN, and any for any contract developers or admins you've had or change your credentials and settings in a way that refuses access to anything you can't clean.

It's much harder to tell exactly how something came to exist on the system after the metadata is destroyed. Some web hosting companies have good free incident response in their security departments, like HostGator.