There two types of patches:
Base system - Includes kernel, system files and core apps such as BIND, Sendmail etc.
Apps / Ports - Applications such as apache, postfix, mysql and much more installed using ports.
To patch base system in binary mode use freebsd-update. This works great if you are not using custom kernel. See tutorial: FreeBSD Update Software and Apply Security Patches
To patch base system using source code (build world) use make and cvsup commands, see tutorial - FreeBSD cvsup: Update The FreeBSD From Previous Releases Using Source Code
To upgrade packages and apply patch use:
Code:portsnap fetch extract pkg_version -l '<' portmaster -Da