I've had very good luck using Front Panel Express software to lay out my panels. I've cased up a Millet and a Steps in Hammond cases with metal panels and I haven't mis-drilled a hole yet. I lay out the panel just like I was going to have a panel made, and then print it on paper, cut out the panel outline, and cut out the holes. Then I tape it onto the case and put the panel parts in to make sure everything fits and everything has clearance over the board parts, etc. I also make sure the holes are the right size, or at least almost big enough- to the point where a little reaming will make it fit perfectly. My motto is: I can always make it a little bigger but I can't put metal back on the panel.
When I am sure it is right, I print another copy and just cut out the panel outline and tape that to thte panel and drill it out.
A good office supply store will sell heavy copy/printer paper that is almost the consistency of very thin cardboard. I think it is 90lb or 100lb paper but don't have access to it right now. That might be useful for larger panels, where paper is too flimsy to accurately keep it's position.
I was very concerned about my ability to properly center parts, especially board mounted parts like the Millet pot shaft. No problems yet...
I bought a 15/16" Greenlee punch for those Neutrik jacks. It is very expensive but it makes nice smooth, professional looking holes.
Regards,
Neil