To me, it would make the most sense to put it in
/usr/local/etc/X11. For now, however, I still keep mine in
/etc/X11. I would at least like it there rather than just
/etc because it really doesn't fit in with the rest of the configuration files. Also, I tend to keep several different xorg.conf files and flooding
/etc will all of them would be poor file housekeeping.
As long as X.org is still reading it and the location of the file makes sense for you, put it whereever you want. When it comes to helping newbies, though, I think it is best to go with the location that *most* users would expect to find it (of course that's based purely on what I think *most* users would expect
).