It really depends on the type of games you are going to be playing the most.  The most common layout is the street fighter, a joy with 6 buttons in two rows of three buttons.  The other common layout is NeoGeo, joy with 4 buttons in a arc.  There is also a merge of these, a joy with 7 buttons, standard street fighter with the 7th button along the bottom row next to the joystick.  The bottom row would be for NeoGeo with the 7th button not used for 6 button fighter games.  See the X-Acrade control panel for an example of this setup.