Consider that you need to upload to the server insane huge files where normally a file uploader would have a script timeout. Well so far the only way to work this out is by using a FTP (which you would have to give access to) and upload the files to a server and them process the files, but things have changed. It has just been released a stable version for PHP-GTK.
PHP-GTK allows you to create GUI applications portable for Windows, Mac and Linux and with this you could create a GUI application for uploading files to the server where whithout having to create access for each user. Pretty cool right !?