Use the tocbibind package by Peter Wilson.
LaTeX does not by default list the Bibliography (or the Index, or the Table of Contents itself) in the Table of Contents. This package remedies that.
In the preamble:
\usepackage[nottoc]{tocbibind}
Be aware that tocbibind's default behaviour is to also add an entry for the Table of Contents itself to the Table of Contents. If, like me, you don't want that, you have to use the [nottoc] option to the package to disable this behaviour.
An email correspondent recommends the JabRef bibliography reference manager, a dedicated, cross-platform application for managing BibTeX bibliographies. I have no personal experience with this software, but if it had existed when I was writing my thesis I certainly would have given it a try — it looks very promising.