The BKWorks Products Multi-User File Manager is our most popular product. It is based on PHP / MySQL, and has a vast variety of security deeply implemenented into it.
Specifics: User Logs In - their password is encrypted in the database using the industry's leading one-way encryption, SHA1. Next, when the user uploads a file, the file is uploaded into the 'uploads' directory. The filename is encrypted using random variables (the time) and the original filename, once again using SHA1. The file is then stored in the database as the user's file.
All the files have a unique header that determines whether or not it's being run by the home script. If it's not, it redirects, and the user is sent back to the homepage.
The download script checks to make sure the user is either the original owner, or an administrator. If they are not, the script shows the help page describing the error.
License
This project is released under a proprietary-type freeware license, NOT OPEN SOURCE. Please read the license here before downloading and using.