You can also extract your notes (and notes alone; the 2.5 firmware did something to change the way highlights were stored) for all your Mobi books, Amazon-supplied or not, using MBPReader
which outputs a plain text file.
This might be more convenient on a single-book basis than digging through MyClippings.
It also still works on both notes and highlights made on Kindle for Mac (and presumably K4PC), but it turns out you can't use the .mbp created on K4Mac on an actual Kindle.
Although if you drag an .mbp file along with the book from Kindle to K4Mac, then you can see your Kindle-created stuff on K4Mac as well.