I like the custom cables since it makes for a much cleaner presentation. I try to make the output somewhat intuitive to the original pinout. Something like this for example.

Neo-Geo/Genesis 1/Master System

original -> new
1. Mono Audio - > Audio Left
2. Ground -> S-Video C
3 Composite Video -> no change
4. +5v -> S-Video Y
5. Green -> Component Y
6. Red -> Component Pr
7. Composite Sync -> Audio Right
8. Blue -> Component Pb