I had never heard of JoytoKey until it was mentioned in this thread. Then again, I haven't needed it so I had no reason to search for it. As soon as I have Xbox360 controllers (or my X360/PS3 hybrid arcade sticks) plugged in, the games recognize them as the input source. At most, I'd need to select "controller" in the games' options menus.
The only times I've ever had to use another piece of software were when I was using a hybrid control scheme (controller on the left, mouse on the right). For that I just used the Logitech Gaming Software that came with my gamepad/mouse.