You'll get lots of opinions on this, so let me start. First, if you want to use packages you should use the -stable repository. Otherwise over time you will be limited to the packages that were available at the release (such as 6.3, for example). See the -P flag on portupgrade. If you must use a package, see that it is available first.
I don't use pakages much, and honestly am surprised that it takes you two to three days to update Gnome. The whole thing takes about eight hours for me, and my system is pretty old.
On upgrading philosophy, I try to avoid "portupgrade -a" whenever possible. Usually I track a few major metaports, such as xorg and gnome, and a bunch of smaller ones. The metaports often require attention from /usr/port/UPDATING, but between minor versions usually a "portupgrade -R" gets all the pieces. So if you work top down, -R does it. Only rarely do I start at a low level and build everything depending on it unless it is something like gnutls and UPDATING instructs one to do so.
The other thing you have to answer is "why do you want to upgrade?" Certainly you have to on a somewhat regular basis, but there really is no need to do so that often unless you need a new feature or are fixing a bug. I've found over the years that I usually introduce as many new bugs as are fixed, so I limit my updating to once every two months or so on my desktop system unless I am chasing something I need (like the recent moused issues with xorg). Monsters like openoffice I only do when they break, which is usually once every year. I almost never update ports on my servers unless I *really* need to.
It is also useful to learn how to use HOLD_PKG in /usr/local/etc/pkgtools.conf.
Some ports too require tools other than portupgrade. ImageMagick seems not to work with portupgrade any more (it reports a broken Makefile) but portmaster works fine.
For me there is a lot of art involved with updating if you have a lot of ports installed like I do. So every two months or so I leave a day on the weekend to update the whole computer. It mostly works on the first shot, but there are always a few that need more digging. Others do it differently, of course, but I've managed to keep things going pretty well since 4.8 was cutting edge.
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