In the end, you're going to have to figure out what's most comfortable for you, but to find that out I'd suggest using a template for an existing game. I did quite a bit of research on this by downloading manuals for conversion games. Here's some links to the better ones (Joystick-to-button measurements are measuring from center-to-center):
CAPCOM 6-button layout - Used on Street Fighter II and others. Joystick is 4" from first button (center to center) and buttons are 1-5/8" apart.
Download it from this pageNeo-Geo (SNK) - First button is 3" from joystick, 1-5/8" apart. This I measured on my own dedicated cabinet.
TMNT: Turtles in TIme (Konami) - First button is 3-9/16" (91mm) from joy, Buttons are 1-7/16 (37mm) apart
Primal Rage (Atari) - First button 3.5" from joy, buttons are 1.5" apart. Measured this on my dedicated cabinet, but the drilling template for Guardians of the 'Hood is the same.
Altered Beast (Sega) - Buttons approximately 3.5" from joystick, Buttons are 1.75" apart. They are an unusual (but decent) layout. They kind of look like this:
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This layout was used on most 2-player system-16 games (golden axe, e-swat)
Most manuals can be downloaded from here. There is also a nice archive of manuals at
www.crazykong.com/manualsFor most classic games you can find the manual at one of those two places.