What you want is to use PLUpload. http://www.plupload.com/ You add that to the page to have the uploading and then set the target to an XAgent which grabs each file and then you do what you want with them. PLUload handles multiple files at a time - in a queue really. The XAgent process them 1 at a time. But again the user is dealing with multiple files.
I'm trying to get it on NotesIn9 but I just haven't because I completely suck... but I will get it there.
There should be a working example in here: https://bitbucket.org/leedy/filevault if you can't wait and want to dig around.
Let me know if you have any problems or questions.
Dave
NotesIn9.com