Its a combination of personal perference, and what kind of games you will be playing on your cp. I loved the Virtua Fighter 2 layout of 3 buttons in an arc (customized to match my thumb, index and middle finger lengths). I also liked the Soul Edge/Soul Calibur 4 button layout which is exactly the same as VF2 but with one more button in line with the 3rd. Lastly I like the 6 button in a row fighters (ala SF2) and the 4 button fighters (ala Tekken). I do not like the neo-geo 6 button arcing...because I never played on those cabs before.
So I ended up with a 6 button cluster in a row (ala SF2), and then 2 more buttons arcing downward off the left like VF2. With this layout I can play VF, SF, SC, Tekken just like the arcade. Playing classics with the thumb and index finger button is also preferable to me in this setup.
Here is a pic of my cp, its hard to see but the last 2 buttons in the row are black. Lower 4 colored buttons are for Soul Calibur, first 4 color buttons out of the 6 are for tekken, and the 6 in row are for Street Fighter type.