Hi Oskie,
yes, my forespeakers are right: The emergency stop should work in a way that does not need the Software or even the Computer.

But remember: the parallel port is using TTL logic, so you have to provide a defined logic state to the pin, i.e. either 0 Volts or 5 Volts.
If you just connect a switch to the input pin and to ground pin, you can generate 0 Volt (switch closed) but with the switch open you generate an undefined state... there is only noise coming to the input pin, but no 5 Volts.
A simple solution would be a switch (connected to the ground), together with a pull-up resistor (connected to 5 Volt). (Computer ground, not the one from the drive power supply...) And only do this when you're sure what you are doing... especially the good old parallel port is very easy to damage.

See also:
http://en.wikipedia.org/wiki/Digital_signal(hope you don't call me a teacher

)
Konrad