Howdy all, I am just doing a new build and I have been thinking through my EPO circuit and limit switches. 

Should my limit switches (these are *not* home switches) cause an EPO condition (which means spindle shutdown, stepper power supply shutdown, etc.) or should it just be hooked to mach and have mach do a software stop.

What sort of machine?

My plasma just kills the torch, stops all motion and goes into E-stop mode if a limit is tripped while running.

Its a Milling Machine.  I guess I should have the limits trigger an ESTOP, which means the whole thing shuts down.

I think i would do that as well.

If it was a commercial machine, the limits would kill power to everything.
It's really up to you, and how safe you want it to be.

Triggering the Estop relies on the software to stop everything. This is no different than just letting the limit input stop the machine. Both are relying on Mach3 doing it's job.

This is probably how at least 95% of hobbyist mach3 users do it.