So this is the basic idea, more so I don't forget but any input/comments always welcome.
Create a mini CNC for drilling PCB's, it would require...
Building an X/Y Table similar to Geir's (sorry can't link, using a Tab). Instead of a pump hook up a 12v motor with a drill bit adapter
Mount the motor so it can move on the Z axis, either on a spring with a servo to push it down, or threaded rod like normal CNC mechanics. Use the handy TIP120 for switching on/off. (2.2K resistor, Diode)