Highlights is a Mac utility for extracting PDF annotations and converting them to portable formats (Markdown, HTML) or archiving them in Evernote. When you open a PDF in Highlights the highlighted text, comments and image selections are extracted. If it is a journal article, the app fetches metadata for it automatically and embeds it in the PDF. You can then open the neatly formatted highlights in Evernote directly as regular notes (ENML-files). This way, you can have a PDF library on disk and an easily searchable summarized archive in Evernote.
Highlights can also be used for working with PDFs and notes in sync. You can highlight text and select images in the PDF, have them extracted in real-time and then add comments to the extracted highlights and have them synced back to the PDF as PDF comments. To simplify literature reviews, Highlights will lookup references you underline in the PDF and link them if possible. For more information check out the website highlightsapp.net.
The app is available in the Mac App Store for 9.99$, but I have some promo codes to share with you, so grab them while their hot: