Holes.  Anywhere.  Any Size:  Absolute Positioning. 

When a simple hole is needed and you don't have the right Forstner bit or hole saw or paddle bit to cut the hole, the CNC can be used as a drill press. Your CNC cuts what you want relative to the 0,0,0 home point you have set both in your drawing used to create the tool paths and on the board where they will be cut.  The standard strategy when laying out cuts is to set the home/origin point at one corner or the center of your project board. Shapes are assigned coordinate points relative to that 0,0,0 origin.  In your CAD software draw a circle the size of the hole you want, being sure it is centered around 0,0,0 on your drawing. The size of the holes can be precisely measured down to the precision your CNC is capable of, usually .001" or ,002".   Create and save the profile or pocket tool path to cut it out.  Now at the CNC, simply move the bit to any center mark where you want that hole.  Zero (set to 0,0,0) the machine at that point.  Run that hole tool path file.   You can move , re-zero, then cut the same hole as many times as you need it now without going back to lay each out on the overall board. Cut the same hole at different centers, on different boards.  Router end mill bits are commonly available down to 1/16" in diameter and 1/4" to 5/16" in cutting length.

Good for through holes so long as you have a long enough router bit. Great for flat bottomed holes with no center divot that Forstner or paddle bits usually leave. Great for dowel holes no matter how much your dowels have swollen or are out of round.

Some CNC controllers have geometric primitive shapes (circles, squares, etc.,) built into them for easy/quick cutting without using any CAD software. 

If you have a way to clamp your boards/project at any angle/compound angle underneath your 3-axis CNC then any size of a hole can be "drilled" at nearly any angle through them.  The limiting factors are Z axis travel and spindle/chuck angle clearance above the bit.  

Perfect Wood Plugs. You can buy plug cutters in a variety of fixed sizes.  But when you've accidently picked up a 11/64th drill bit for your counterbore instead of the 3/8" bit you intended to use you most likely won't find a plug cutter for the resulting hole.  With a CNC and a scrap of wood to match or intentionally contrast your background wood just draw a circle the size of the plug you want and then use 1/8" end mill to profile cut it outside the line. Don't go much deeper than you want your plug to be in length, then you can pop the plug free with a screw driver.  To ensure a tight fit you could even taper cut these plugs.  See Tapered Holes below.

Tapered Holes.   The hose attached to most shop vacuums has a tapered end on it. When making jigs or connecting adapters to attach that hose to, a straight hole makes an imperfect (loose) opening for that tapered plastic end.  The fluting tool path in Aspire and VCarve Pro can be used to taper the perimeter of any hole. Match the tapered hole in your jig/adapter to the taper of the hose end and you'll have a snug fit that won't vibrate loose or pull out easily.  You can even use the CNC with a circular array of short vectors and the fluting toolpath to make perfect tapered holes for small tapered alignment pins.  Making a chair composed of spindles and planes?  Consider tapering all the spindle ends and holes they plug into. Done right the joints will continually wedge together under normal loads.

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