I've done a quick check of how annotations (the text-based kind) are stored, and it seems it's just plain XML with start/end markers, plus any text you added... the biggest trick is probably to use those markers to extract the actual text from the document.
Disclaimer: it's early here, so maybe I'm completely missing the point
Edit: maybe I should add that I'm on Ubuntu, so I don't use the Sony software at all... I've recently been using my PRS600 for research too, and highlighted a lot of stuff I want to quote... I'll see if I can't hack together something that can read the XML and export a text-file or something.
This would actually be perfect to build as some kind of Calibre-plugin... but I'd need to give myself a crash course in Python for that first, and time hasn't been all that abundant lately.