I use a program called Evernote. This is a great little program. I use it…
0049 iBooks Highlights into Evernote
With all iBooks you can add your notes and highlight text. With some iBooks you can share the highlights. This allows you to send the highlighted text to your Evernote database.
This does not work with all books. It appears that the author can choose the ability to share, meaning that some books allow sharing and others do not. You will not find out which ones do until you try it.