It depends on what you are using UAE for. I mainly use the workbench and programs associated with that. In this case you would first of all like to install picasso 96 and let the amiga belive that UAE has got a graphics card attached. This gives a huge speedup (And nice screen resolution). At the same time I like to give all the horsepower to the CPU and I choose the oldest chipset setting (ocs). At the same time allow as much memory to the JIT-engine as possible.
Dont know if this is the best sollution but im faily pleased with it.
