Some time ago, I started writing a windows tool for extracting annotations and highlights from the database (cf.
this post). Since I learned later that annotations are also available in xml files I did not continue this project. The tool is therefore in a raw state, but working. Feel free to use it at your own risk.
Edit: new version uploaded (22.03.2013)
Edit: new version uploaded (27.05.2013)
Edit: find the latest version
here.