For what it's worth PaperDesk has an update today that also launches it's online service that appears to be free. From within PaperDesk you can sync all notes with their online site "myPaperDesk.com". Your notes then appear there as well. You will eventually be able to download your notes as a pdf from the web site.
The site also says that it will store all uploaded docs - including those that you have already deleted from your iPad.
The online site is free but there appears to be no way of editing the docs online (as of today) -- not sure what the future holds.