Writing to parallel port with minimum latency
Have a look at www.LinuxCNC.org.
The purpose of this linux distribution it to drive step motors for DIY CNC machines.
The linux kernel was patched to add kind of limited real time behaviors.
One way they use to control the motors is... the parallel port.
The kernel has dedicated real time routines that run every xxx us with reduced jitters in order to drive the motor drivers.
The kernel also embed all the logic needed in case that you want to add some kind of PID controls to your motors.
But.. I don't know how well it scales if you have to control 1000 motors...