Actually, the latest version of ibooks does offer two ways to export notes:
- Via e-mail.
- Via PDF provided you print to an app like printopia (Mac) or a virtual printing solution (PC).
If you need the PC solution, please respond and I will research it for you.
Also, Nook in conjunction with Nookstudy (Mac/PC) may have this feature.
The people on the web are recommending iAnnotatePDF, which can export annotations as text. They say the interface is not that great.
Possible untested Nook instructions are below:
To use the Nookstudy options:
1. Download Nookstudy. Import the PDF.
2. Ensure it shows up and can be read on Nook for ipad.
4. Go back to Nookstudy. Your changes will be there. Then, export the notes to a .doc file. (supported.)
I would also take a serious look at Readdle's products and Goodreader.