Skim has a "Take Snapshot" feature which allows you to print anything which is visually on the page. It also has a "Convert Notes" feature which turns PDF annotations into "skim notes" which you can then manipulate.
There is a really simple yet robust tool for extracting highlights, notes and images from your pdf-files available at: http://www.sumnotes.net . Not only it supports various advanced features like exporting to DOC and TXT formats, but it also allows you to send extracted highlights into your Evernote account or email. All desktop browsers and operating systems are supported. We are in cloud, so no installation is needed. Try it out.
I faced the same problem. To resolve it I created a free service to extract annotations from PDF to CSV: http://exportpdf.info . It exports only sticky and text notes, it does not export highlights and images. You can edit/print CSV files with any major editor like Microsoft Excel or LibreOffice Calc.