BibTeX is a text-based format for managing citations. Similar to Endnote, it has some distinct advantages, being free is not the least of these. Unlike Endnote, the database is stored in a normal text file, greatly decreasing the chances of becoming corrupted. It is included with all major TeX distributions. Using an editor for .bib files makes life a lot easier than trying to do it all in a text editor. BibTeX is well implemented in LaTeX and more recently OpenOffice. Word support is still poor. For Word documents, I transfer my files to Endnote via the bibtools utilities.
These are scripts to use with Bibdesk that downloads articles for JSTOR automatically, that fix cites against JSTOR. There are also scripts for capitalizing titles, downcasing, and protecting titles.
Here's a great list of tips on basic bibliographic tasks that are a bit of a puzzle in BibTeX, like how to order unpublished articles properly, how to print uncited material, how to deal with non-standard author names, and how to force capitals in titles.
