This is mostly a note to myself but in case it's helpful to anyone here's what I do:

1) First, cvsup:
# cvsup -L 2 /root/ports-supfile

2) Back up the package database:
# cd /var/db
# tar cvfz var.db.pkg.tgz pkg

3) Check for consistency:
# pkgdb -F

4) Then, list outdated ports that have a newer version available in the Ports Collection with the pkg_version(1) command:
# pkg_version –vl '<'

5) Read /usr/ports/UPDATING

6) Upgrade one at a time and make sure to install dependencies:
portupgrade -R [pkg name]

Good references:
http://www.freebsddiary.org/portupgrade.php
http://www.freebsd.org/doc/en_US.ISO8859-1/books/handbook/ports-using.html