gigertron, a member of this forum, posted a video of him controlling the desktop, and surfing Reddit with an eye tracker and a game controller (http://www.youtube.com/watch?v=2IjTZcbXYQY – http://developer.tobii.com/community/forums/topic/gaming-and-desktop-mouse-control-with-the-rex/). Eye gaze is for instant large movements, and the joystick is for fine movements.
Perhaps in a FPS, you could let the eye tracker warp your aim to an opponent, and then if required, the joystick could take over for finer control of the aim.