To be honest, FCEUX was not built with OS X in mind. I have never owned an Apple product (other than an iPod) and most of the FCEUX developers are PC-centric as well. However, the SDL port is actively maintained and once I managed to succeed at compiling it on OS X and I was playing Castlevania on OS X. A few commits later and FCEUX was actually quite usable on OS X. The problem was that it was difficult to obtain all of the tools and libraries required to build FCEUX. On Linux systems, grabbing the compiler and libraries are a yum/apt-get/pacman command away, but it was not always this easy on OS X.
Enter Homebrew. Homebrew is a source-based package manager for OS X with ruby-based packaging scripts. I'm no Ruby expert, but the documentation made it easy enough for me to put together a script to patch FCEUX to make it OS X compatible and to actually compile and build FCEUX. If you have homebrew installed, you can build FCEUX and the necessary dependencies with the following command:
brew install fceux
If you want to compile a command-line only version, you can use this command:
brew install --no-gtk fceux
Currently, the emulation window and the GTK GUI window are in two separate windows due to a limitation in the OS X X11 implementation. I have not yet tried Quartz yet, but it might work properly in a single window with that. Keep in mind that FCEUX was not originally intended for OS X, but SDL and the rest of the libraries utilized by FCEUX are available for OS X.
As always, patches are welcome. If you run into issues first check the website and file a bug on the sourceforge tracker if necessary. Feel free to drop by #fceu in irc.freenode.net for any fceux-related discussion.
Here is the Ruby "Formula" for FCEUX in Homebrew's GitHub that I wrote if you want to check it out. You don't need that link if you want to build FUCEX however -- you can simply use the brew commands above