Pro Controller
I used to belong to a group that did real time air traffic control for people who were flying on MS Flight Simulator. There is a program called squawkbox that runs over MS FS that allows a player to file a flight plan anywhere in the world and then fly it using ATC from people playinga game called ProController. You can get both from Vatsim.net. Follow the links down the left side of the page to find the downloads for squawkbox and procontroller.
One caveat...it is time consuming, and full of people who have their own ideas of how ATC should be run. It got to be too monotenous for me that I just deleted all the programs and said forget it. It's been a while since I was part of it. Maybe it's changed. I hope this was something like what you were looking for.
