Two problems here:
1) The minor one:
you provide no information. The possibliites are as varied as are all the machines in the world.
2) The big one:
You don't do emergency stops in software. The Estop should always be hardwired. Its not a soft stop. Its an EMERGENCY stop. The industry practice is to use redundant contactors and a hardwired contactor monitor circuit. However, I recommend you monitor your EEstop devices with the PLC so that the program knows to go ahead and shut off the outputs to everything that was shut down by the hardwiring. Its also usefull to annunciate which estop device was actuated.
I typically wire all devices needing inclusion in the estop system to the same output Card(s). Then the output power for those cards is supplied from a source that is switched off when and Estop device is tripped. You will need to do a thorough evaluatin of your system to determine what should be on the estop system and what should not be. If you don't know how or are not sure, then you need to get some help. Somebody's finger, hand, or life could be at stake. Don't take it lightly.
Other sources of stored energy besides electrical must be accounted for: mechanical, springs, gravitational potential energy, compressed air, hydraulic, water pressure, steam, momentum (braking may be required), latent heat, chemical energy, etc. Whether these are hazards or not is entierly dependant on the nature of the equipment.