I've just tried running my Python code under JIT compiled PyPy instead of interpreted CPython. It was a lot slower by about 50% which is odd as PyPy is supposed to be a lot faster due to the JIT compiler. While I appreciate that there could be many causes, the Raspian distribution of PyPy is now getting a bit long in the tooth. Any chance of updating it to 2.6 or higher in the distribution please.
Just FYI, my code uses I2C, GPIO and RPIO (for DMA PWM) and after a simple rebuild to make their PyPy libraries, they work well.