Different games have different gamma levels. Some per-game settings are unavoidable.
You could also just change commandline args such as brightness, gamma, etc.
For example, mame.exe kof98 -gamma 0.5 -brightness 0.4 works.
The nice thing about just putting those things in the command line when you launch the game is that you have no dependency on MAME cfg files. You could nuke a directory and still have all your settings.
I also highly recommend using MAME's volume arg to normalize the sound across different games. For example, this will run the game at -11db:
kof96 -volume -11
As far as INI files go:
MAME takes things such as horizontal.ini for all horizontal games, vertical.ini for all vertical games.
You can also use the name of drivers. neogeo.ini will apply to all Neo Geo games, and cps2.ini will apply to all CPS2 games.