Before I'd asked my question, I didn't know about upstart. For those interested, upstart is an event-driven (instead of a state-transition driven) replacement for the old "System V init" system.

To get to the point and skip the documentation, have a look at the /etc/init folder. You'll find several .conf files in there. Editing these files allow you to control at which runlevels different services come up and go down. These include samba4.conf, which was the main one I was concerned about (as this also controls ldap, kerberos, etc).

I initially went to /etc/init.d/rc2.d and wondered why there were no entries for samba there.

Just to confuse the issue, bind9 (along with other services) is still configured via the old system V init scripts in /etc/rcx.d, so, I rm'd /etc/rc2.d/S15bind9 and made a symlink K15bind9 to the same target in /etc/rc2.d/