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Debian sysv and Ubuntu non-upstart services
On Ubuntu 12.04, upstart boot scripts can be identified by their entries in /etc/init.d being symlinks to /lib/init/upstart-job.
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echo manual >> /etc/init/service_name.override
Debian systemd services
Reference
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systemctl disable service_name.service
Reference
General
http://en.wikipedia.org/wiki/Init
sysv
From Securing Debian Manual section "3.6.1 Disabling daemon services"
Quote:
| ... the files under /etc/init.d are configuration files and should not get overwritten due to package upgrades if you have made local changes to them |
Based on that, any disabling technique that leaves at least one /etc/rc*.d/[KS]* symlink which is different from the symlinks in the upgrade package should be fine.
Upstart
http://upstart.ubuntu.com/cookbook/
systemd