http://wayland.freedesktop.org/gtk.html says: 
"Your application must not use any API in the gdk_x11_ namespace or any raw Xlib calls."

Many applications still copy libegg code so this is probably the place to start. Please add dependencies bug report numbers to track progress in depending apps.

$:andre\> grep -r gdk_x11_ .
./libegg/smclient/eggsmclient-xsmp.c:
      gdk_x11_set_sm_client_id (xsmp->client_id);
./libegg/smclient/eggsmclient-dbus.c:
      gdk_x11_set_sm_client_id (ret_client_id);
./libegg/smclient/eggdesktopfile.c:
    launch_time = gdk_x11_display_get_user_time (display);
./libegg/smclient/eggdesktopfile.c:
  gdk_x11_display_broadcast_startup_message (display, "new",
./libegg/smclient/eggdesktopfile.c:
  gdk_x11_display_broadcast_startup_message (display, "remove",
./libegg/treeviewutils/eggaccelerators.c:
  xmodmap = XGetModifierMapping (gdk_x11_get_default_xdisplay ());