What reference manager is the best option?

Managing references can be a major pain in the butt. It’s one of the more annoying parts assembling a manuscript, especially when you have to reformat after a rejection.

So, what’s the most efficient way of managing references for a manuscript?

Some of the options people use are BibTeX, Endnote, Mendeley, Papers, Reference Manager, Zotero. Or you could just keep a big list of references in a word processing file.

At one point, many years ago, I used Endnote. But they end up releasing new versions of the software twice as fast as new editions of Campbell’s Biology and it’s just stupid to keep paying a company over and over for the same damn product. A sucky, glitchy, hard to use product, by the way. If you’re not using Endnote, for the love of some deity, don’t let yourself be tempted.

I’ve been looking for a New Way for the last year or so, after year or two of doing it old school. I’m writing in Word to share files with collaborators. And I’m not paying money for a program that will go out of date next year. Both Mendeley and Zotero are free. But Mendeley was bought by Elsevier last year, which has a number of downsides. I thought I’d go for Zotero. But I had a difficult time importing my old endnote library (and my endnote version expired and wouldn’t let me do it, long story). In the Mendeley there already are a huge set of collected references, and its integration with web searching for new citations is super-smooth.

So, I went with Mendeley.

Two weeks and one manuscript later, I think it’s coming along pretty well. It plays nicely with my version of Word and crashes infrequently enough that I haven’t yet damaged my laptop by punching it.

As far as I can tell, a lot of folks are using Mendeley. But I’m really curious to see the results of the poll.

Any thoughts about reference managers, what works and what doesn’t, and if you’ve changed from one system to another, any good ideas? Or unsubstantiated opinions?

Nota bene: If you write your manuscripts in LaTeX, I don’t think I can really handle hearing even more about its awesomeness. I take your Word for it.