http://www.shipsim.com/ShipSimForum/index.php/topic,4505.0.html
This link will take you to some interesting comments about controllers, including a link to a site that is advertising a commercial controller that would be ideal for ShipSim (it's not out yet). I use a Logic3 star fighter joystick but I only use it for fast vessels and small ones, (Pilot launches and the Red Funnel Cats). Even then I revert to the keyboard and mouse when docking. I only use the throttle for 'both engines ahead', a button for 'both engines astern' and the joystick for port/starboard. I had considered taking the joystick apart and using the USB interface board and other components to make my own controller but when I saw the link above I thought I might wait and see what happens.
Regards, DaveM