I guess I'll have to voice the lone pro 'opto-isolation' opinion here. Opto-isolation is useful for far more than protection from getting things hooked up wrong the first time. When properly designed it will electrically isolate the computer from the machine. The primary advantages of this isolation are noise reduction, electrical protection of the host computer and interfacing dissimilar voltages. In some cases this isolation is essential, and in some cases not.
I built an opto-isolated breakout board for a Dyna-2400/Mach III conversion I did. It used all the original drives on the machine. The opto-isolation insured that no noise from the steppers/drivers got fed back to the computer. When I was looking at commercially available boards I was surprised to see some that seemed to have a single onboard transformer to provide power to both sides of the opto-isolation circuitry. That kind of blows the whole point of opto-isolation.
I'm finishing up a Mach III conversion of a Bridgeport Discovery 308 VMC now. It uses a Galil motion control board and ICM-2900 'break out' moudule. The encoders, limits, homes and operator interface buttons are not opto-isolated. They are powered by the ICM-2900/Galil and in shileded cables. The 'extended I/O' which controls both 24VDC and 110VAC. This was done through 'Opto-22' racks, which hold individually opto-isolated SSR's. This completely iso-lates all the higher voltage and 'noisy' signals from the control.