Managing literature and the many citation formats for publications requires computer support. I've been using Endnote for years, well over 100 publications were done with it. However: upgrading the word processor nearly always entailed buying a new copy, 'twas difficult to use in the group, a little hassle to synchronize for work at home & office, no unique hash for each entry (rather a meaningless entry id, easily leading to doublets). Also the programmers did occasional serious missteps. There are a number of alternatives: Citavi, Zotero, RefWorks, Reference Manager, Papers, … My needs were: group capability, seemless Mac OS support, reliability, ease of use, breadth of citation format support. With the help of a colleague and his group (thanks, Uli) we compared. For me #Zotero was the clear winner; for my colleague it is slow, don't really know why – possibly size: I have 2000+ citations, he has ≈10,000.
I like #Zotero http://www.zotero.org/ : it's a Firefox plugin, which is a good start, and it also has a stand-alone app (for Mac OS, Linux, Windows). The nicest thing: the database is on-line, on your disk you have a synced clone. So you can work from any computer, and on a train! Getting stuff into it is also interesting: have a webpage open in Safari, Firefox or Chrome which contains citations or PDFs: these are recognized as possible records and imported on a click. This is free as long as you stay below 100 MB – sufficient, if you're not storing your PDFs there. Group facilities are also fine.
There is a huge number of citation formats (too huge, but that's an error of publishers who cook too many formats), and it's possible to roll your own, if difficult. I made one as I like them:
1. Citation in the text as (name, year)
2. Bibliography with the least possible number of commas, dots and semicolons.
It was possible, though a hassle. Finally: Establishing the in-line citations and associated bibliography works with any *.rtf file, there are Word / OpenOffice / LibreOffice plugins, and there's synchronisation with BibTex (“AutoZotBib”), so the bright people using Latex are also happy.
I managed citations of my last 3 papers with Zotero, and it went rather smoothly. Currently, I have only 2 gripes: there is a little synchronisation issue behind our Med School firewall (but easily circumvented), and there is no real hash -- but a useful "Duplicate items" detector.
Legalese: Zotero is a project of the Roy Rosenzweig Center for History and New Media, and is funded by the Andrew W. Mellon Foundation, the Institute of Museum and Library Services, and the Alfred P. Sloan Foundation. So it is currently paid for by foundations, thank you!