The code that I provided to Andrew Vallums was expecting application/octet-stream. However Internet Explorer and Opera were sending multipart/form-data. This would not work with the servlet example I posted since the handling mechanism is considerably different.
Alan O'Driscoll and I discovered the differences using Wireshark to sniff the packets and see what was being sent over the wire. As a result, I have written a new servlet to handle the differences between browsers.
The example application I wrote has a number of different examples included with minor variations on the theme. The version most folks are interested in is example #6 which uses the ajax-upload, and the new servlet. Here is the Apache Maven project which was developed on NetBeans and tested on GlassFish v 2.1.1. Here is a link to the project: ApacheFileUploadEE5.zip.
Here is another resource for file upload plugins: 9 Powerful jQuery File Upload Plugins. I discovered it while I was looking for something else.