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I use BibDesk [1], which is open source and comes bundled with MacTeX. It is useful and very fast by itself, and it has a full AppleScript API which makes it extendible without having to dig into the code.

I wrote a couple of 'plugins' for it, one for looking up papers through Alfred, and another for quickly importing papers from the arXiv and from INSPIRE (the high-energy physics database).

[1] http://bibdesk.sourceforge.net/

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I'm also a big fan of BibDesk. I used to use Papers 1, but it was always a little buggy. Then the paid upgrade to Papers 2 was a big kick in the shins (paying to upgrade to an even buggier program with some features removed).

I tried Zotero standalone and Mendeley also, but the switch to BibDesk was a fresh breath of air. If you're using a bibtex workflow, I highly recommend it. It isn't the prettiest program out there, but it is fast, stable, and functional.

I started with Mendeley (used it all through my masters) and have gone entirely to BibDesk for my PhD. I keep .bib files in git, and sleep very well. For writing papers, I use biblatex-chicago if I have a choice. My workflow might look old to an outsider, but to me it feels dependable--an elegant weapon for a more civilized age.

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