Well, it's more a matter of how your parts need to fit as well as the printer settings. inside diameters tend to print under size. The amount that the print is off will depend on your printer and filament settings. I would say it's trial and error, mixed with designing for your intended material. I have had to rework entire assemblies for the sake of printing the objects rather than machining them.Also, toss in a fair amount of calibration as well. SD machines tend to make oblong holes and bosses out of the box, so dialing in your belt tension and stepper motors will help.

+1
Since I.D.s will generally be more prone to being undersized than mating studs, I will usually upsize the I.D. of the hole by about 0.5%.  Seems to work pretty well for me...