As file managing plugins, this one seems to have pretty much everything one needs. Simply upload files to a special directory (either through the browser, or via FTP for huge files), and it does pretty much everything: assigning files to categories (which will be directories on the server), id'ing files according to type, assign permissions to each file or category, and so forth. It works both from the admin backoffice and from the front-end, via shortcodes and widgets, and includes simple-to-modify templates for your users to upload and retrieve files according to the permissions. Then you can use the uploaded files in your own posts and pages, just like any others. In effect, this comes close to be a complete Media repository replacement with access given not only from the backoffice but also from the frontend.
Files do not need to reside locally in the same server: they can be pointed to a different server with just static files, like Amazon S3, and a cron tab can be launched to keep them all in sync. This is pretty much everything you need to build something like a media repository for your users, where WordPress is just the frontend dealing with instructions, registration, and permissions, while WP-Filebase handles the rest. You can even fine-tune the bandwidth allowed for each user group for downloding files.
There is also a Pro version (paid, but cheap) including even more functionality.
There are only two caveats. The first is the time it takes to sync all the files with the database. Since this relies on calling system functions externally (namely, id3 and md5), for huge files these time out pretty easily, preventing sync to work at all. But it's exactly to deal with huge files that WP-Filebase allows FTP uploads. If you have lots of small files (like, say, a website just with pictures and text documents), WP-Filebase will easily deal with them. If you have just a few files with several GBytes, then sync will very likely fail.
The second issue is that this is not meant to be a replacement for an e-commerce shop selling digital files. While I've not tested things out, it might be possible, thanks to the shortcodes and the built-in permission system, to use WP-Filebase with a third-party e-commerce solution and embed the files on the shop articles, but unless you have full control over what gets uploaded, this might not be the best plugin for doing that. On the other hand, if you're doing a file repository where users upload and share files among themselves — be it on an intranet, with different user levels and so forth, or even on the public Internet, where registered users have access to some files, while unregistered ones have access to others — then this might be just the right plugin for you.