The /etc directory is reserved for configuration files that are local to your machine. No binaries are to put in /etc. Binaries that were in the past put in /etc should now go into /sbin or possibly /bin.
The X11 and skel directories should be subdirectories of /etc:
/etc |- X11 +- skel
The X11 directory is for X11 configuration files such as XF86Config. The skel directory is for ``skeleton'' user files, which are files used to populate a HOME directory when a user is first created.