When I was messing round with lr-dosbox about a year ago you could control the mouse using the gamepad analog stick. I think this is exactly what you are looking for.
@gohakn - Did you ever find a solution to this... getting this down would be awesome because I too have a very complex joystick (ipac2 with spinner, 2x 8way, 1x 4way and a trackball... getting this ability is essential for ikari warriors, guerilla warfare and discs of tron etc.