It completely depends on what joystick you have, whether you're installing in wood or metal, the length of the shaft, and how high your want the joystick to come up. It also depends on what type of games you plan on playing.
For example, dabone mentioned that he routed out the top for his t-stick plus. This is how I had my Supers.
However, I'm going to just screw my t-sticks directly into 3/4 wood from underneath without routing. This will keep the ball top low to the control panel. Of course, this is for a classics cocktail cabinet.
In other words: different application -> different mounting method.