I rarely bother using the CNC router to automatically drill any PCBs I make, but these were an exception - three boards with over 250 holes each. I had previously cooked up a program to convert Excellon drill files from Eagle into G-code suitable for running on the CNC router, so (once I figured out how to use the program again!) it was a relatively simple matter to set it up. The spindle is an air-powered pencil grinder and I'm using standard carbide PCB drills.
I again used my webcam crosshairs to align the board.
The alignment came out pretty good, considering (as I found later) that the X and Y axes of my router aren't exactly perpendicular, for some reason.
Video of operation. You'll notice the drilling sequence isn't exactly optimised - the drill goes all over the place. However it's quick enough that I'm not too bothered.