Skim

I recently discovered (as in: a colleague suggested this to me) the freeware app Skim for the mac. This is a great little tool for taking notes within a PDF file that I find much much more usable than acrobat pro. Also, the notes are stored in the file-system, not in the actual PDF so that you can then email the pdf to a colleague or student without the notes.  It supports attaching notes, highlighting, circling / labeling, a presentation mode, and a host of other handy little tricks.