As pointed out by a few people in Hacker News thread, my first benchmarks were performed with PyPy1.9, so I have updated the test runner to use the latest PyPy 2.3.1 and PyPy1.9. I have also removed the micro-benchmarks, and now only include benchmarks from the Unladen Swallow test suite.
PythonJS (with the fast-backend) is faster than CPython in four of the following five benchmarks. Some may argue that this is not a fair comparison because the fast-backend is only a subset of the Python language standard. Keep in mind that: 1. it is large and useful subset, and 2. PythonJS is designed to allow you to mix both modes with in the same script by blocking out code as fully compliant or fast using special with blocks or calling pythonjs.configure.