You can create folders to organize files to up load, as you do on your hard drive.
You can use your integrated search engine to find files quickly. This will be much easier if you tag the files with certain keywords or add them to an appropriate description.
Each file can be downloaded, commented (ideal if you share the file with other people) and even previewed in the case of images, videos, documents, etc..
In addition, Box.net is related quite well with other web tools like Picnik or Gmail, so we treat our files almost as if on a hard drive.