I found the iCommand 0.5 software and it's exactly what I am looking for to do some project work. I've managed to be able to talk to the NXT brick through a USB Bluetooth adaptor, although it's connection is sometimes spotty. I was hoping to be able to use a hardwired USB cable. However, no matter what COM port I set the icommand.properties file to look at, it doesn't seem to be able to find the NXT.
I assume that this is because I'm not talking over a Serial Port when using the USB cable, where as the Bluetooth adaptor presents itself to the system as a virtual Serial port.