I think the API and abstraction should be better thought out to be just 1 js file include instead.
Other comments:
Good use of FileData and multipart builder for handling multiple browsers. However I thought Firefox also supported sending files with FileData() object, so why is xhr.sendAsBinary necessary? As far as I know, xhr.sendAsBinary is not in the w3 draft and is being deprecated by Firefox, as it's a FF proprietary method. Perhaps that part of the code could be removed?
Even though MSIE and Opera have no support for Drag & Drop, multiple file selection or upload progress indication, I'm really pleased to see such a well thought-out file upload plugin that doesn't require the use of Flash.