Extracting PDF Highlights
If you have the money, Adobe Acrobat has many features that let you view and print all of your annotations (notes, highlights, etc.). Although not significantly cost prohibitive most people (myself included) don’t really want to spend money if you can find a comparable free or open source solution. Adobe Acrobat Reader (the free version most people use) does allow you to view the highlights in a summary pane, but doesn’t allow you to extract and print (You’ll notice that if you don’t create the annotated note with your highlight the entry will show blank.) The best free PDF viewer that I experimented with is Foxit Reader and it allows you to easily create a PDF summary of your highlights. Simply go to Comments -> Summary Comments and you’ll be prompted to save a new PDF file that only contains the highlighted text along with the page number.
UPDATE: The above solution does not work (as attested to in the Comments section and by yours truly) however, one of the other Commentators recommended GoodReader. Now I just happen to use that application on my iPad and it created a wonderful synopsis of my highlights for a document that was resisting the ZotFile plugin.