For those who want to export notes but not quite sure how to do it as suggested by David ( it's not that the explanation is unclear, it's just that I have zero experience with this kind of stuff).
1. Go to
http://www.sqlite.org/download.html and download the following zip:
(Sorry I only know how to do it for Windows)
Precompiled Binaries for Windows
sqlite-shell-win32-x86-3090200.zip
(364.10 KiB)
2. Unzip it and go to the folder you just unzipped
3. Inside the folder, create a New Text Document (don't rename it yet)
4. Open the New Text Document and copy the following:
Code:
%~dp0SQLite3.exe "E:\.kobo\KoboReader.sqlite" "select (case when datecreated=maxdate then ('<b><i><u>' || replace(volumeid,'file:///mnt/onboard/','') || '</u></i></b><br />') else '' end), max(datecreated, coalesce(datemodified, 0)), text, coalesce(annotation, '') || '<br />' from ( select *, (select max(datecreated) from bookmark where volumeid=bm.volumeid and (text<>'' or annotation<>'')) maxdate from bookmark bm where (text<>'' or annotation<>'') order by maxdate desc, volumeid, datecreated desc )" > "%~dp0annotations.html"
pause
[/QUOTE]
Be careful with the directory. Match them as below:
5. Click save as and name it extr_annotations.cmd. Plug in your Kobo device.
Make sure you have the following files. I think the New Text Document is not necessary.

7. click extr_annotations and you're done!!
8. There will be a new annotations file