Been looking around at parts and pieces for a CNC machine. This structure works for whether the machine is for machining, sensing, or RepRap FDM. Your basic mill/machine will be a three axis machine. X-Y and Z. My preference for linking these machines together is to use the table on an in-out Y axis, then the main gantry left/right for the X axis on the cross member, and the milling head on a Z axis. Easier and capable of "reaching in" is if the milling head moves for Z. If the supports are moved, the mechanics are more complex (as you have to keep the two axes even) but the whole machine is stiffer.
Now, beyond the basic 3 axes, we can add more. One is doing both Z axes options. This lets you reach and achieve stiffness as need be. Rotary axes are the next useful axes. A worm gear based rotary table makes wide circular machining. A horizontal axis lets you work a lathe style mechanic into the system, but you'll need a driver and driven ends.
Many multi-axis systems start adding axes at the cutter instead. This is simpler from a mechanical aspect on larger machines, but always useful. Starting at the Z axis, putting on two more rotary axes to allow for machining withing a hemisphere, and can be very useful. However, a smaller or less forceful cutter is needed. However, you also need a very accurate motion system since you only have 180 or 360 degrees of motion, instead of, say, 1/16" of motion per rotation.
I'm considering a CNC cutter head. Around here, Menards has a low cost rotary tool with flex head. By mounting the flex tool, the cutter head can be kept small and light, allowing for good maneuverability on a small machine. Flat and ball mills can be used with 1/8" shanks, but I'm considering starting out with a carbide or high speed steel Dremel burs. These are more like small mill bits but have 12+ cuts. They also cut at dremel speeds (8000-25000rpm) which is well above what many mill bits are rated for. If a saw is needed, Dremel has some somewhat expensive but neat "EZ Lock" blades that make them quick change and indexable.