Apple - Export pdf annotations only using preview?

I'll second that answer. I'm doing the same with PDF Expert instead of GoodReader. It is really important that you do the conversion in Skim on a COPY of the original PDF, as otherwise the PDF expert (or GoodReader, I assume) will lose the annotations, once converted (e.g., if you have your PDFs in Dropbox, which you then open either on the iPad or Mac). There is a slightly more elegant solution though. It's trivial but it avoids making a copy of the PDF:

Open the annotated PDF in Skim, convert to Skim notes, export notes to text or RTF, an then close Skim without saving. Your original PDF with notes will stay unconverted (and thus still annotated for GoodReader), but you will have your notes and highlights exported and saved.

As I said, trivial...

You may want to have a look at the "PDFs>Extract PDF Annotations" Automator action.

There is a really simple yet robust online tool for extracting highlights and notes from your PDF files available at: sumnotes.

Not only does it support various advanced features like selective extraction or predictive extraction, it also allows you to save extracted highlights into TXT or DOC files. It supports all browsers and operating systems and does not need any installation. It's free, too.