Yeah after reading the top posts I thought immediately of Elite. A plane for the XY and a drop line to the Z.

Has anyone got a Zaon (.com) galactic system map link handy ? I have an image here and its beautiful though presumably copyright so I wont post it. Its the way to do it but I cant find a link on the site to any of their galactic maps.

Most stars sit in a plane around a galaxy so the only really important 3D nature is the relation between galaxies of which you wouldn't use a linear drive to get from one galaxy to another so the exact coordinates seem a bit pointless.

I think traditional mapping techniques break down with star systems.