Chris
There are, as you will find here, many approaches. The one I use for really accurate hole location is not to mark out at all, but to find the edge(s) of the metal with an edge finder and to located the holes by co-ordinate drilling. I have a 3-axis DRO on my milling machine, which is all I ever use for metal drilling, and this method locates the holes within 10 microns or so.
It also helps to start the holes with a centre drill; since these are so much stiffer that a normal drill with the same point diameter, so there is less chance of it wandering. To be really anal, follow it up with a stub drill (about half the length, so about 8 times stiffer). Make sure the drills are sharp, with even lips, and don't let the flutes clog up.
Before I used the DRO approach I used an optical punch, which was pretty accurate, but not as good as the above method. Any method relying on locating holes via a punch mark cannot of course be better than the initial marking out; the best method for this for most home users is probably to use a surface plate and height gauge.
David
Edited By David Littlewood on 01/06/2012 19:26:25