I've just finished reading ReWork: Change the Way You Work Forever (which is very good by the way) by Jason Fried, David Heinemeier Hansson and used the kindle app on my iPhone to do so.  As I read I highlighted some bits, and added notes to others.  This was great functionality, and at least I could see those notes using the kindle website.  

Prior to using this app, when reading a book and making notes, I've been using toodledo to store them in.  That way I can read them using the appigo notes app or the toodledo app.  Ideally I wanted to get my notes/highlights from this book into toodledo to join them.  A quick google led me to the NoteScraper applescript script which exports highlights into evernote.  I don't use evernote much anymore, but still have it installed, so fired it up, went to the kindle site, navigated to the page containing my highlights and notes for ReWork and ran the script.  

Because I want to get one text document for all my highlights and notes, I choose "All notes in one" at the first dialog box.  I enter "kindle" as the name of my notebook, and chose default tags from the next two dialogs.  When the script is completed, I'm left with all the notes and highlights for a book in an evernote note, which is easily copy and pasteable into a text file, or into toodledo notes.

Update: Whilst this worked, it wasn't ideal, so I rolled my own (Mac OS based - uses applescript)