well here is a list of a few files:
/etc/X11/XF86Config - most systems default configuration for mouse/keyboard/monitor/video card
/etc/X11/XF86Config-4 For some reasona lot of distros are adding -4 to the end of the file, go figure.
~/.xinitrc - This file is called by startx to run your windows manager and desktop manager/combo therof. (~/ means home directory) examples are gnome, kde, enlightenment, etc.