1. Never store a backup or archived version of your website in a web server’s public readable directories.
2. Do not leave files that you do not want to be read/indexed/searched/downloaded in the web root.
3. If it is absolutely necessary, make your hosting provider disable directory index generation for that directory.*
4. Password protect directories that contain sensitive information.

* Directory Indexing is a feature of mod_dir, an Apache module that will generate a list of all files in a directory if there is no index.html/php/etc file found in that directory. This is most likely how the archives are being found by Google Code Search.