Yes I am part way through writing a Processing app that will generate Gcode files of holes of various sizes and shapes. I used it to cut some hexagonal inlays in some MDF so nuts could be recessed into a block of MDF that was then bolted to the work area. This allowed me to mill an area flat so I could compensate for a slight tilt in the axis that resulted in a 1mm difference in height between each ends of the X axis.
The program generates round, hex, square, oblong, D shaped and notch shaped holes. This is a screen dump of the D-Shaped holes showing the tool diameter.
There are also some applications that design front panels and produce DXF files, so I am writing a DXF reader and translator into Gcode. I wouldn't have to do this if I could get some of the free Gcode generators working but all the ones I have tried don't work on my mac. I am also too mean to pay money for one especially the silly money some people ask for them. When they are finished I will put them all on line.