Does anyone know how to enable the joystick as the primary means of control? I can use the mouse if necessary, but I would prefer to use my joystick with this game, and I can't figure out how to make it work. Any help is appreciated.

In the launcher, there is a Audio/Joystick tab, click on that. There should be a drop down box at the bottom, underneath the sound option and you should be able to select your joystick (ensure it is already plugged in though)
If you can't select it and you have the joystick plugged in, you'll have to force the game to recognise it by selecting the registry tab , but I cannot remember which registry line you edit, you should be able to find that information elsewhere within this forum.
Hope this helps!

What launcher?

Never mind, problem solved. All I had to do was set the joystick as my controller of choice in the control panel, and then do the same in the launcher. Thanks for the help.

I also had this problem.. with windows 7. Game ran great and windows recognized the joystick but it would not function within the game.... solution for me was this:

in windows: control panel, hardware and sounds, devices and printers, choose controller, (right click for) game controller settings, advanced, "select the device you want to use with older programs" the joystick.... doing this solved both Independence War AND FreeSpace, Both had the same problem

what "control panel"?