One of the first thing I did was adding a mechanical limit to the Z-stage.  The  X & Y motors with the belts are not strong enough to cause any damage if hitting the mechanical limits.  I do worry about the Z axis causing damage since it has the screw pitch advantage for added force.  For safety I added a clamp on the lead screw that
creates a safe limit if everything else fails. See Picture:

For accurate zeroing I added an opto-interrupter that is repeatable to a few microns, much better than the stability of the wood frame and table mounting.

See: http://www.vinland.com/Opto-Interrupter.html

I have the opto set so it triggers about a mm above the table so I never need to worry about hitting the table.  I have in the software turned off the limit switches and only use them for homing.

Then in the startup code  I have:
G28 X0 Y0                 ;move X/Y to min end stops
G28 Z0                    ;move Z to min end stops 
G92 X0 Y0 Z0.95 E0        ;reset software position to front/left/z=0.0

Tweaking the Z value will allow fine adjustment of the table without trying to fiddle with moving microswitches around.