So far (besides the custom one I built and use now), to me, a joypad with analog sticks, seems to work best, with all possible ships in the game, since it has 4 axis, some pads more than that, plus the pov hat, and lots of buttons.
So my money would be on joypad. And then a decent one, with as much axis as possible.
My custom controller cannot really handle azipods and such, so on the side, I use one of these, which is a quite nice one, with 6 axis. and you can program certain button combinations, giving it many more functions.
http://www.thrustmaster.com/product.aspx?ProductID=82&PlatformID=5Fred
