[HuFlungDung]

Andy,
You have not told us what kind of a system you are thinking of building. If you are using a stepper drive, then these most typically are "open loop", meaning there is no feedback provided to your computer that the system has made a move correctly.

The computer sends pulses to the motor, expecting that they are perfectly executed. Backlash in such a system could be factored out by estimating how many steps are required before motion begins to execute correctly in the opposite direction. This is not a true elimination of backlash, but merely is compensation for it. Mechanical loading of some sort (gravity, springs, etc) can sometimes also work to always keep the load against one side of the gear train, and eliminate the effects of the backlash.

The only risk is that at some point, Murphy's law will execute, and the mechanics of the system will change and cause the backlash to suddenly appear (a slide begins to stick, or a tool lifts the part unexpectedly across the backlash distance).

A servo system using encoder (linear scale or rotary disk) feedback to the control operating in "closed loop" mode means that the control checks that the movement commands were obeyed, and adjusts the machine position by commanding further movement until the scale readings jive with the commanded position. So, if the encoder is reading the motor shaft angle directly, then the backlash in the output gear train is not compensated, whereas, if you take the encoder off the motor, and mount it directly on a ballscrew, then the angle of the ballscrew can be accurately detected. The motor will then be commanded to rotate the gears until the ballscrew is correctly positioned, regardless of any backlash in the gears.