MySQL uses a different mechanism other than apache2, so you can simply comment the three lines inside “/etc/init/mysql.conf”

Change this:

start on (net-device-up
and local-filesystems
and runlevel [2345])
stop on runlevel [016]

to this:

#start on (net-device-up
# and local-filesystems
# and runlevel [2345])
stop on runlevel [016]

Source: http://anonir.wordpress.com/2010/08/09/ubuntu-lucid-disable-services-from-starting-during-boot/

It worked perfectly with the latest version of Ubuntu as of this article (Oneiric, 11.10)