Dictate Note Annotations
The voice dictation feature in Mountain Lion opens up the possibility of quickly adding note annotations to a PDF. To add a text note annotation to a PDF opened in Preview.app, use the Tools menu > Annotate > Note command. Use the voice dictation feature (shortcut fn fn) in 10.8 to dictate the note. Continue adding note annotations to the PDF, and use File > Save a Version (CMD S) to embed the notes into the original PDF.
Export PDF Annotations with PDFoo
Next, open the PDF in PDFoo, assign a prefix, and export the PDF annotations to a text file. Each note will be followed by a pdfoo:// URL which links back to the original PDF. Follow the link to lookup the context for your note. Save your exported notes in Evernote/Scrivener/DEVONthink for easy search and retrieval, or share it with your colleagues via email or the web.
Like to Dictate? Get Dragon Dictate
OS X 10.8's inbuilt voice dictation feature has a few shortcomings currently: it has to connect to Apple servers for processing which introduces a noticeable lag, it doesn't quite work well with accents, and it requires keyboard intervention to switch it on and off repeatedly. For users who find the dictation feature useful, Dragon Dictate for Mac v2.5 (currently $80 on amazon) is a worthwhile upgrade which addresses the above limitations.