How important are software updates to you?

freebsd-update is for updating the base system. For updating the ports, there is a portupgrade utility and portsnap utility to update the ports tree. For binary only updates something like "portsnap fetch update" followed by "portupgrade -a -PP" should do.

What I'm wondering is, if you installed the apps as precompiled binaries, are the apps different than if you installed them with ports? Or would a ports update NOT change any of the pre-made binaries?

Ports is somewhat customizable in its build methods (like passing $CFLAGS to ./configure). Pre-built binaries are intended for any platform that can run FreeBSD, so they tend to be generic.

(I failed to mention that for FreeBSD the conf file should be modified to point to stable repository instead of release one to get the updates). In addition to the above, precompiled binaries usually lag behind the versions in ports and sometimes by quite a bit. For some packages (like sun's version of jdk) there may be no binaries so ports is the only option.

Due to customizations possible in ports, mixing packages and ports can cause dependency problems. Another possible issue could be that a newer package may overwrite older version of the app built from ports with custom options. In my experience a good approach is to always use ports for apps that are built using custom options, and packages/ports for others (portupgrade -aiP in FreeBSD chooses package if available and falls back to ports otherwise). It requires occasional manual intervention though and works well if the number of customized packages is small.