There's no standard system-wide xmodmap file. It depends on your distribution, on your display manager and on the user's desktop environment.
In Debian, I think all display managers run the global session startup scripts in
/etc/X11/Xsession.d before they invoke the user's chosen session startup. So does
xinit. As of jessie, this does not include any call to
xmodmap (presumably because the default keyboard configuration is supposed to be done via XKB), but you can add your own script there.
You can put XKB settings in
xorg.conf, but you can't reference an xmodmap file.