I have a basic MS Sidewinder joystick, and neither version of the game seems to acknowledge it. I've calibrated it in Windows, and it still isn't picking up in game. I haven't been able to get it to work in Wing Commander games either. Any ideas?

Strike that. I fixed it.

Absolutely -- Don't try to trick your games into using a keyboard as a mouse. The solutions you use might take precedent over the actual controller you find at Goodwill for $3.