Workflow for annotating PDFs
Skim.app is a free, open source Mac OS X app which is great for annotating PDFs. In particular, the Text Note tool provided by Skim (shortcut CTRL CMD 1) allows you to draw "sticky notes" on a PDF page and write comments. Skim does not modify the original PDF directly, and annotations are kept in extended attributes, i.e. hidden information attached to the PDF file on disk. To ensure that these annotations do not get clobbered when syncing PDFs via Dropbox or a similar application, make sure to turn on "Automatically save Skim notes backups" option in Skim Preferences. This will create a small-sized .skim file adjacent to the original PDF to hold all the Skim-created annotations. This is a reliable way to annotate a PDF on multiple computers using Skim, since only the small-sized .skim file has to be synced across computers.
Export PDF Annotations with PDFoo
Skim can export a new PDF with embedded notes (i.e. annotations) using the File > Export menu command. Open this new PDF using PDFoo, and export annotations with pdfoo:// URLs that provide a context for each note and allow you to jump back to the source PDF.