Endnote is sinister bloatware, incapable of love and human warmth. It deserves to be shunned.

For references, I've recently gotten interested in BibDesk, which, as far as I can tell, would be jesusware if only I knew LaTeX. But I don't. So, based on the comments here, I guess I'll be having another look at Mellel + Bookends. Sente sounds great, but when I downloaded the trial, I found it slow as molasses (manymanymany beachballs of death) and buggy with respect to database searching. If anybody can convice me that this was all my fault, I'd be thrilled, b/c if Sente really worked like it says it does, it'd be great.

As for note-taking, I don't mean to be jerky, but really, this almost seems like a pointless question. Notetaking style varies greatly between people, and there's a huge array of options available, so I'd recommend you take notes in whatever texteditor suites you, and then organize them post-hoc in whatever file management tool suits you. And btw, if you're talking about note-taking in class, then the tools you should be using are pen and paper. The clackety-clacking of people taking notes on laptops in a lecture irritates the shit out of me, and I won't allow it in my classes.