I use PAL for both the desktop and my games. I like the increased multiplier on the desktop for a less flickery screen on a CRT, but many games suffer from this. I have to use the config tool manually to switch the rate when I want to play them.
It would be great if the config tool accepted command line parameters to work its most important magic without opening its interface. Then things like the multiplier and scanlines could be controlled from scripts and WHDLoad could automatically switch down to 50Hz and back for games.
I also think it would be neat if the functionality of the tool was isolated in a shared library with a documented interface, so third-party user interfaces could be built. I'd like a MUI GUI myself.