Just to clarify:
most opamps we use want to have a dual supply - so +xV AND -xV. inputs and outputs sit at ground level.
For use with a battery we fool the opamps into believing it has a +/- 4.5V supply by introducing a *virtual* ground at 4.5V. That's Vref. Stick that into the + input of an opamp (through a resistor), and the rest of the pins will follow - have a look at some schematics and you'll see. The opamp thinks Vref is "ground", and the battery's poles sit at -4.5 and +4.5V.
This does create the need for coupling caps - they pass signal while blocking any DC offsets - the opamps ins and outs can now sit at Vref without any DC troubles for the rest of the circuit where signal is referenced to real ground.
Edit: read everything you can find on polarity protection and designing bias (or Vref) networks at GEOfex.com.
This scheme is the more or less standard one, which will protect you pedal from reverse polarity - briefly.
Reverse polarity will result in the diode shorting out the reversed voltage, keeping it from the rest of the pedal. This will immediately turn into a battle to the death between diode and supply, either frying the diode (subsequently letting the reversed voltage rampage through your circuit) or frying the supply. There are better ways.
Also - depending on the wah circuit, this may not be the circuit needed. Do you even need Vref?
