A few more thoughts on the web client.
-Fall back non-java upload option (even if it is only one file at a time)
-Inform the user somehow about their lack of java software (rather than java tools just not working - maybe a note upfront about the use of Java)
-Based on the user/folder permissions change the status of the toolbar icons (grey out uploads/create directory etc if required)
-As mentioned previously offer a more windows explorer like view (folders on left and files on right)
-some reference to who is logged in.