There are a number of additional dependencies required for getting things installed on OS X. Starting with a blank slate OS X machine, this is the process it takes:
# Install Xcode Command Line Tools
# Install Homebrew
ruby -e "$(curl -fsSkL raw.github.com/mxcl/homebrew/go)"
# Some deps
brew install node spidermonkey closure-compiler yuicompressor
brew install llvm --with-clang
cd ~/Repos
git clone git://github.com/kripken/emscripten.git
One of the nice pieces about this script is that it ensures that (just about) every utility used by Emscripten is in $PATH, making .emscripten not entirely necessary.