One of the reasons for confusion on this seemingly obvious question (where's the conf file) is that those of us who've been running X on Linux for a couple of years have been through some changes. Even before the transition to XFree86 v.4 there were occasions where more than one conf file was involved in a sort of cascading effect.
Most distros seem to have gone back to the single file now, but the practice still appears to be to include a LOT of different configuration options and have X sort out what works and what doesn't. My curent file, for instance, is unusually simple and only has four mode sections - only one of which works.
A while ago I embarked on a quest to get my system running in 100dpi mode instead of the default 75dpi. I found many places where the setting was available, but none of them affected my actual X sessiosn at all. I eventually gave up on it - it doesn't really seem to matter anywhere except when printing graphics.
I'm sure more than one of us anticipated a far more complicated problem, and did not trust the simplicity of the obvious answer. Hopefully Leo will let us know if we were wrong.