The native support provided by the HTML specification only allows the ability to upload one file at a time. In other words, the user would have to take action for each file.
In order to provide the ability for the user to choose a directory and upload the entire directory, you need to code an applet or ActiveX control. With either approach, I believe you would have to sign the applet or control so that you may read the user's hard drive.
Check out http://www.jspsmart.com/, they might have what you're looking for.