Bibliography software also known as Reference Management Software automates one of the more mundane parts of scholarship: making sure you adequately attribute and cite your sources.
Endnotes is the most common in the Windows world and probably humanities world too, but in the world of science and mathematics Bibtex based on TeX typsetting system created by Stanford computer science legend Donald Knuth. TeX is probably one of the first open source software projects, starting in 1978 and predating the Open Source movement by a long, long time. Here are some additional points:
1. Citeseer the open access academic paper repository and search engine for the natural sciences uses Bibtex.
2. BibteXML translates Bibtext into XML form which makes it easy to sort, regroup, and reformat bibliographies.
3. It would be really nice if bibliographical tools could be combined with other text processing computer programs to support philological analysis of texts. The Warring States Project had a wonderful site on philology that will eventually be back up I hope. Many of the Burmese and Mon texts that were published ages ago as edited volumes may in fact have much more complex textual genealogies, genealogies that actually might take a lot of work to untangle.