Skim.
I've long been dissatisfied with Apple's Preview program, which is OS X's main software for reading and handling pdf files. It's got no highlighting feature, no integrated note-taking (you can leave stickies, but that's not the same), and generally offers just about no ability to manipulate or mark up the text. That said, I don't like Adobe's Acrobat either, which is too big, expensive, and slow for my purposes. Enter Skim, a freeware pdf viewer with absolutely terrific mark-up capabilities, You can highlight text, and the notation is saved to a sidebar listing all your highlights along with the first few words and the page number. You can leave various types of notes, circle areas to come back to, etc, etc. And it's all free, and elegant, and fast. Why Apple hasn't packaged something similarly powerful, I don't know. But for now, use Skim.
