A basic run-through of how to fully upgrade a gentoo box
Run emerge --sync to get the latest package index
emerge -1u portage to ensure the package manager is up-to-date.
Upgrading the System
emerge -uDN --with-bdeps=y world to upgrade the system fully
dispatch-conf to resolve any config file changes
Cleaning up after an upgrade
emerge -ac and verify the output looks sane before executing to cleanup no longer necessary packages.
emerge @preserved-rebuild to rebuild packages linked against obsolete shared libraries.
perl-cleaner --all to rebuild any perl packages using an old perl version.
Portage can run into a whole host of dependency errors, requiring manual intervention.
Most of the time, the error output tells you how to fix things, but for more complex cases you may have to consult some of the gentoo-fanboy alumni.