I recently became aware of Skim, a PDF Reader and note-taker for OS X made by the team behind BibDesk. Skim is designed to help reading and annotating scientific papers in PDF, or what they say: “Stop printing and start skimming”.
While v0.2 of Skim didn’t contain much more functionality than what’s already available in Preview, v0.3 starts to become interesting. Particularly the possibilities to save and print the notes taken separately. Skim also integrates lovely with BibDesk which, of course, is no big surprise considering their common origin. Skim is still in the early stages of development, but it looks very promising so far!