Recently I was working on implementing support of joysticks and gamepads, and now it may be considered as 'ready'. This is my test configuration (Logitech Extreme 3D Pro, 3D Connection SpaceNavigator, and XBox360 controller):

Now SE supports up to 16 controllers simultaneously. You can assign each axis and button for any action in SE (axes can be assigned to 'analog' actions like rotation or aileraons control, buttons - for any, including 'analog' ones). This is the screenshots of new controls menu. In the first tab, 'Common controls', almost nothing changed, except that 3 new columns was added for binding the joysticks buttons (yes, you may bind any button for any action):