I don’t like or dislike upstart or whatever system service management facility, however, I do hope Ubuntu can give me a single solution to handle system service.
So to disable a service, you can try System-V style:
update-rc.d apache2 disable
or upstart style:
echo manual > /etc/init/cron.override
or try chkconfig though it’s less common on Ubuntu. Sure, you may want to check /etc/rc.local as well for auto-start services that are not system service.