Step 1: Strip SNES controller cable
Alternatively (what I did), you could replace the SNES cable with one from something else, that way you don't need to chop up the controller. In my case I had a broken NES controller that I borrowed a cord from. It is also recommended that instead of cutting the cable you get a SNES controller extension cable and cut that up. In either case the steps are the same.
Step 2: Powering the controller
To draw power from the parallel port attach a diode to pins 4-9 on the parallel port connector according to the diagram below. The +5V end attaches to the white wire on the controller (make shore that the diodes are aligned correctly, the black stripe should point away from the parallel port).
Otherwise you can strip a spare USB cable and attach the controller's power (white) wire to the red 5V wire on the USB cable and the ground (brown) wire on the controller to the black/ground wire in the USB cable.
Step 3: Attach everything else
Step 4: Install software
PPJoy has fairly good documentation, including instructions on using different interfaces (the Playstation or Sega Genesis controllers for example). But here is generally what you need to do.
After installing PPJoy go to the control panel and click on the icon labeled "Parallel port Joysticks". In the new window click on the button labeled "Add...".
In the "Configure new controller" window set "Parallel port" to "LPT1", "Controller type" to "SNES or NES pad", "Interface type" to "DirectPad Pro/SNESkey", "Controller number" to "Controller 1", and "Controller sub type" to "SNES or Virtual Gameboy".
Hit "Add" and let windows install the drivers.