Organizing your literature and references are an important part of your thesis work. If you are using LaTeX, you will benefit from using the BibLaTeX reference tool for processing your references and bibliography.
The BibLaTeX database
The references are collected in one or more files with the extension "bib", e.g. "references.bib".
There are programs for handling bib-files directly, e.g. the free program JabRef which can be found for the Mac, Windows and Linux platforms.
Editors like Emacs and Vim both have extensions for handling BibLaTeX references.
Be sure to use the UTF-8 character set which usually is standard on most platforms. In some instances you must configure your LaTeX software to use this. See below.
In addition the biber program is used for processing the references, no longer bibtex. This must also be configured.
Character set and biber
Configuring BibLaTeX on different platforms depends on the LaTeX editor you are using. Below you can find links to procedures for one editor for each of the platforms Linux, Mac and Windows.
There are many other LaTeX editors, see LaTeX Editors/IDEs.