from the big thread about the Que, I believe it was determined since it has a capacitive touch then you can use a stylus but it needs to be a special one designed for capacitive panels. from looking at the pen accuracy is not going to be very good. And from everything I read, hand written markup is problematic at best and impossible at worst for some document formats if not all of the supported formats.
Someone suggested a blank document which you could then write notes in, which is effectively a journal but you need to be sure and add a LOT of blank pages when creating the book, depending on the subject because once you create it there will be no way, on the reader, to add more pages. Still a simple utility app could be written to auto generate a journal for the Que device, heck if it can be done that might be a nice feature in Calibre for any reader with a touch interface that has no way to create a separate file for hand written notes.
I think there needs to be more info about the Que before anyone considers it usable as a productivity tool.
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