Zen, don't mind tcd, he's a n00b. Anyways, I don't think theres is a program that works with a joystick. I'd recomend using the keyboard and mouse. Everything is handy, and availiable.
There are game controllers that you can use with this game but Sidewinder is not one of them. Using the mouse and keyboard is the best option. It won't take you long to get used to it. If you don't like the default key assignment you can change them to whatever you want. A game controller will serverily limit your options when playing. There is a thread on this forum somewhere (do a search) that describes which controllers will work with MOHAA. Good luck.