I don't know if anyone else has figured this out, but I gotmy joystick to work with Freelancer.
I used a Saitek X52 flight controller set up so that the throttle was my speed (full forward was cruise; quite neat, and I thought quite clever of me : P), and the joystick itself was the mouse (I don't know if you can do that with every joystick). The problem was then getting reverse pitch (that is, pull back to go up, forward to go down). After a few hours of searching and testing, I found the Joymouse 2.1 program, which has an option to reverse axes; just flipping the y axis was enough for me. (Joymouse 2.1 here :
http://www.download.com/Phatsoft-JoyMou ... ag=lst-0-7 )
I do feel, however, that it is still much easier to control the game with a mouse; recentering with a joystick is a pain, and after a few hours of trying to fly a light fighter with my flight controller, I hooked up my shiny new Ebay-bought trackball, and had a lot better of a time.
Maybe with a different setup, or a slower-moving fighter (eg: not a Startracker : P), it would be more fun, but I'll stick with a mouse. Still, I felt itwas important to point out this way of using a joystivk in Freelancer. Cheers!