sh /usr/ports/Tools/scripts/mergebase.sh
This script will attempt to backup /usr/X11R6 into
/usr/tmp/mergebase/oldx11base.20071120.140800.tar and then move the
contents onto /usr/local. It will then replace /usr/X11R6
with a symbolic link, pointing to /usr/local. After that,
the script will attempt to change some settings in /etc
that by default point to both /usr/X11R6 and /usr/local
to remove references to /usr/X11R6; specifically, the files
that could get altered are /etc/periodic.conf
/etc/manpath.config /etc/rc.conf.

Be advised that this script expects default environment,
notably it assumes that you have not changed $X11BASE and
$LOCALBASE variables from their default values and that
/usr/X11R6 is regular directory and not separate mount.

If these assumptions are not correct, either edit this script
to change $X11BASE $LOCALBASE and/or $BACKUPDIR values or
do the merge by hand (perhaps using this script as a rough guide).

Enter 'yes' to continue, anything else will exit script: yes
CONFLICTING FILES:
./bin/bdftopcf
./bin/bdftruncate
./bin/mkfontdir
./bin/mkfontscale
./bin/ucs2any
./include/X11/DECkeysym.h
./include/X11/HPkeysym.h
./include/X11/Sunkeysym.h
./include/X11/X.h
./include/X11/XF86keysym.h
./include/X11/XWDFile.h
./include/X11/Xalloca.h
./include/X11/Xarch.h
./include/X11/Xatom.h
./include/X11/Xdefs.h
./include/X11/Xfuncproto.h
./include/X11/Xfuncs.h
./include/X11/Xmd.h
./include/X11/Xos.h
./include/X11/Xos_r.h
./include/X11/Xosdefs.h
./include/X11/Xpoll.h
./include/X11/Xproto.h
./include/X11/Xprotostr.h
./include/X11/Xthreads.h
./include/X11/ap_keysym.h
./include/X11/fonts/FS.h
./include/X11/fonts/FSproto.h
./include/X11/fonts/bdfint.h
./include/X11/fonts/bitmap.h
./include/X11/fonts/bufio.h
./include/X11/fonts/fntfil.h
./include/X11/fonts/fntfilio.h
./include/X11/fonts/fntfilst.h
./include/X11/fonts/font.h
./include/X11/fonts/fontenc.h
./include/X11/fonts/fontencc.h
./include/X11/fonts/fontmisc.h
./include/X11/fonts/fontmod.h
./include/X11/fonts/fontshow.h
./include/X11/fonts/fontstruct.h
./include/X11/fonts/fontutil.h
./include/X11/fonts/fontxlfd.h
./include/X11/fonts/fsmasks.h
./include/X11/fonts/pcf.h
./include/X11/keysym.h
./include/X11/keysymdef.h
./lib/X11/fonts/util/map-ISO8859-1
./lib/X11/fonts/util/map-ISO8859-10
./lib/X11/fonts/util/map-ISO8859-11
./lib/X11/fonts/util/map-ISO8859-13
./lib/X11/fonts/util/map-ISO8859-14
./lib/X11/fonts/util/map-ISO8859-15
./lib/X11/fonts/util/map-ISO8859-16
./lib/X11/fonts/util/map-ISO8859-2
./lib/X11/fonts/util/map-ISO8859-3
./lib/X11/fonts/util/map-ISO8859-4
./lib/X11/fonts/util/map-ISO8859-5
./lib/X11/fonts/util/map-ISO8859-7
./lib/X11/fonts/util/map-ISO8859-8
./lib/X11/fonts/util/map-ISO8859-9
./lib/X11/fonts/util/map-JISX0201.1976-0
./lib/X11/fonts/util/map-KOI8-R
./lib/libXfont.a
./lib/libXfont.so
./lib/libXfont.so.1
./lib/libfontenc.a
./lib/libfontenc.so
./lib/libfontenc.so.1
./man/man1/bdftopcf.1.gz
./man/man1/mkfontdir.1.gz
./man/man1/mkfontscale.1.gz

Files that exist both in /usr/local and /usr/X11R6 have been found as shown above. Merging will not continue.
While some such files are safe to remove as they will be regenerated (like /usr/X11R6/man/whatis), some you might want to move away somewhere safe, and some might point to conflicts in ports.
For this script to continue, you need to either move these files away from /usr/X11R6 or delete them. If you don't know what to do about a particular file, ask on x11@FreeBSD.org mailing list.
The list is saved in /tmp/mergebase.GEny1EFK.