This AppleScript works in the Safari browser, and exports your Kindle highlights and notes directly into your Evernote desktop application.
There are some instructions to follow, which include installing a separate AppleScript parsing utility for “Text search-and-replace commands and regular expressions, scientific computing, folder synchronization.” You must also make your highlights public, as this script works from the Amazon website, not from the My Clippings.txt file.
Once the scripts are correctly installed, you browse to your Kindle booklist at kindle.amazon.com in Safari. Navigate to your highlights for the individual book you want to import. Be sure that you are viewing your own highlights, not the “popular” ones, and that you are viewing the notes for the individual book, not all of your notes for all of your books on one page. Then select the “Export Kindle Notes to Evernote” script from the menu bar. There will be a series of dialogue boxes — which have an unfortunate tendency to A) get lost underneath other windows, and B) take a really long time to appear if you have hundreds of notes. You can choose to export all the notes as one note, or as individual notes, or in a format called “Candel” which may have something to do with mobile devices. You can add tags to your batch of notes, and you can select the notebook that you want to add them to.
After the text is processed, which may take a few minutes, the notes will appear in Evernote, and from there, there are handy methods to export them to other formats.