Currently I use Zotero <https://www.zotero.org/> to organize my
references. Since I do most of my LaTeX writing in LyX
<http://www.lyx.org/>, I use the LyZ plugin
<https://addons.mozilla.org/en-us/firefox/addon/lyz/> to LyX to
integrate Zotero and LyX.
With this setup, I create a separate BibTeX bib file for each writing
project and use BibDesk when I need to work directly with the bib file.
Hope this helps.
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