When I read scientific papers, I mark them up a lot. I underline useful snippets of information, circle reference numbers to check later, write questions in the margins, and so on. Until recently, I was doing this on paper, and then transcribing my notes manually to a FreeMind outline. However, since discovering that I can do all of this and more in Adobe Acrobat, using the built-in OCR scanner to produce text even from scanned PDFs, I’ve gone digital.
Acrobat is pretty expensive, though, especially if you aren’t an official student or faculty at a university with an educational discount. I prefer to avoid lock-in to commercial software, especially expensive commercial software when possible. Anyhow, PDF is now an open standard, with good native support under OS X. I had wished for a long time for a good open-source PDF editor that I could use to mark up scientific documents. Skim is the answer to my wishes.
Skim is designed for scientific reading, and marks up PDFs reasonably well. It is free and open-source software (FOSS if you like acronyms), and comes in Universal Binary and source code flavors. Lifehacker did a brief review of it, as have others if you search the interwebs. I tried it, but ran into one rather frustrating problem. It doesn’t restrict its highlighting to a single column of text. Thus, if you have two-column text, as is found in most journals, it will select across both, totally ruining your ability to highlight a sentence. I don’t know how much of a showstopper this is for others, but for now I’m still using Acrobat. However, since it’s open-source and I think it has a potentially wide audience, there’s a good chance a fix will be made in the future.
For most people who want to add notes to PDFs on a mac, it should work splendidly.