I' m not sure if this is the right place to post my suggestion, but i'll give it a try.
Moodle lacks a funtion to upload multiple files inside the webbrowser (i know webdav provides this functionality..).
So i tried to integrate swfupload (from www.swfupload.org) into the file-upload-site of moodle and
managed to make it work. Perhaps it's possible to take the code and integrate it in future versions of moodle.
You can find a short description of "moodle flashupload" here:

http://www.bildungstechnologie.net/blog/moodle-flashupload-v2-upoad-von-mehreren-dateien-gleichzeitig