Mendeley is a free application designed to manage a large library of PDFs as a list of references (Windows, OSX, and Debian Linux).  It’s aimed at academic users with publications of their own to manage, along with enormous amounts of reading material that are increasingly interacted with only electronically. I use Mendeley pretty heavily–it allows one to comment on PDFs while reading, a la Acrobat Reader or Apple’s Preview, and it’s the only application I know of that effectively organizes thousands of journal articles automatically by author, journal, year, and renames PDF files (which might come from a database like JSTOR with a filename like ‘76348763.pdf’) using the very sensible format “Author (year) – Title.” And it does that based on what it finds inside a PDF, or based on the user’s input.

Would it not be great if the same app that did all of the above also built and managed BibTeX files? Mendeley comes equipped for this, and all one has to do is specify the proper settings in the options panel. Launch Mendeley, then: Tools > Options > BibTeX, and tick all three boxes. Specify a folder in your TeX search tree (typically ~/texmf on Linux/OSX), and Mendeley produces one huge BibTeX file with all of your references! Simply invoke the automatically generated citation keys (in ‘authoryear’ format; e.g., “chomsky1965″) within your (Xe)LaTeX documents, run BibTex and then Latex (times two), and voila.

There is no longer any need for JabRef or BibDesk, or similar, along with that horrid mass of quasi-organized PDFs on your hard drive.

And of course, Mendeley uploads and backs up your files and your citations. Use Cloud or UbuntuOne or DropBox or Box.net (or whatever), and make multiple machines draw upon the same library of PDFs and citations.