The paper is worth a full read as well. One of my favorite bits... "The FCEUX emulator is about a jillion lines of C++-ish code, was intended as an interactive GUI application, contains support for multiple di erent platforms, and the code is, on a scale from a pile of horse shit to not horse shit, approximately a 2"
As one of the major contributors to FCEUX, I feel that the author is misrepresenting the code quality of FCEUX. To be fair, I'd say the code would rate about 1.5 or maybe 1 on said scale.