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)
Create a simple C# program the edits the Drill file for a gerber export (contains XY CoOrdinates), and removes all the unwanted data and sends it via serial to the Arduino.
As the drill file contains the xy from the edge of the board we could minus the lowest x/y from all of the CoOrdinates, so the first hole is 0,0 and all other are the distance from here. (better yet, just find the distance from last hole to the next hole).
The distance on the drill file can be converted to stepper motor step by either the computer or Arduino. Now you could move the drill bit over the top left hole, hit a button and the XY table would move the drill to the bottom right hole to make sure you line the board up correctly. clamp the PCB down, hit the print button and away it goes.Sorry for the bad editing the Galaxy Tab seems to beabitannoying to write a blog on ;-)
So, 2 more months and I'll be able to try make this(All my stuff and myself are in transit from Uk to Australia)