Below is a list of known issues with GNOME 2.6 that are specific to FreeBSD. These are not the only known issues, however. Please familiarize yourself with the GNOME 2.6 release notes.
Other release-specific issues can be found in the general FAQ and the GNOME 2.6 upgrade FAQ.
It certainly is tricky, and you are not expected to accomplish it by hand. Read the upgrade FAQ for detailed information.
evolution-1.4.4 has a problem with attachments under GNOME 2.6. To work around the problem, do the following, as root:
# ln -s /usr/X11R6/share/icons/gnome/48x48/apps/gnome-unknown.png /usr/X11R6/share/gnome/pixmaps/gnome-unknown.png
This problem was fixed in evolution-1.4.5, and upgrading to evolution-1.4.5 is probably the best solution.
gstreamer-0.6.3 doesn't play nice with rhythmbox. It is recommended you build rhythmbox with -DWITH_XINE for now. (UPDATE: As of gstreamer-plugins-0.6.3_1, this problem has been resolved.)
GDM may crash on startup, especially on 5.1-RELEASE and earlier. All GDM users need to copy /usr/X11R6/etc/gdm/factory-gdm.conf over /usr/X11R6/etc/gdm/gdm.conf. The old config version from GNOME 2.2 will not work. Users of 5.1-RELEASE and earlier need to read the pkg-message that comes with the GDM2 port/package on how to patch OpenPAM to work with GDM2.
Gnomemeeting may fail to build if you have ffmepg installed. If you do, remove ffmpeg, then build gnomemeeting, then reinstall ffmpeg if so desired.