The Yellow Paper is a formal definition of the Ethereum protocol, originally by Gavin Wood, currently maintained by Nick Savers and with contributions from many people around the world.
It is a free culture work, licensed under Creative Commons Attribution Share-Alike (CC-BY-SA) version 4.0.
The paper comes as a single latex file Paper.tex. The latest version is generally available as a PDF at https://ethereum.github.io/yellowpaper/paper.pdf. If you find that the borders for links block too much text when viewing the PDF in the browser, you can instead download it and open and view it with a PDF viewer application such as Adobe Acrobat or Evince, where the borders are less likely to display over text.
The paper also comes as a single latex file Paper.tex, which is built as a PDF as follows.
git clone https://github.com/ethereum/yellowpaper.git
cd yellowpaper
./build.sh
This will create a PDF version of the Yellow Paper. Following building, you can also use standard pdflatex tools like http://latex.informatik.uni-halle.de/latex-online/latex.php for compiling/preview.
You can use TeX Stack Exchange; https://en.wikibooks.org/wiki/LaTeX/ (e.g. Bibliography Management and Hyperlinks); and BibTeX editor.
The previous protocol versions are listed in BRANCHES.md.