BibTex
BibTex is bibliographic software used in scientific publication.
Using BibTeX for a math CV’s publication list, blog post.

EndNote
EndNote tends to be used more in the arts and BibTex in the sciences. It is useful for accessing library catalogs and exporting to BibTex format.

OpenOffice.org Bibliography Feature
Using Zotero to manage OpenOffice.org bibliographies, blog post.

RefWorks
Is RefWorks compatible with LaTeX/BibTeX? RefWorks FAQ

Zotero
Math markup in zotero, blog post.