I hate it when I lay out a printed circuit board and discover I haven't left enough clearance around mounting holes to tighten up a nut or spacer with a nut driver, or to even get a spacer in place. This is a simple method to eliminate that problem.

I designed a mounting hole "component" for 3mm or 4-40 screws that include a3.2mm hole or pad plus the clearance for a nut and nut driver in the PCB document layer. These lines, which won't show up on the finished circuit board, show the clearance needed for a nut (where you always want to avoid placing components) and a nut-driver (where it is desirable to avoid placing components). I have two different mounting hole components, one with a pad, and the other with just a hole. 

On the left is the view in the board layout software (EasyEDA in this case), with the nut clearance and tool clearance shown in the document layer (white).  If you look closely, you can see I have text in the silkscreen layer (yellow) extending into the tool clearance area, but not in the nut clearance area, so it will be visible when the board is mounted,

On the right is a view of the finished board.  The nut and clearance outlines don't appear on the finished board since they were drawn in the document layer.  I try to keep traces out of the nut driver clearance area, to avoid any possible damage if a nut driver has a sharp edge.

The dimensions for 3mm / 4-40 mounting hardware are shown below. The are close enough to the same size that the same diameter hole and pattern work for both. A few minutes laying out a footprint like this saves a lot of time during board layout and poor board designs.