Stuff is started using their scripts in /etc/rcX.d/
Where X is the runlevel. So there is a directory for each runlevel.
You should have a script named in format SNN<name> in each runlevel's directory where script is starting.
You remove these scripts and you stop them from starting. There are a few ways to remove sripts.
update-rc.d -f <app_name> remove
Start applications manually by invoking /etc/init.d/<app_name>
Another utility is called sysv-rc-conf.
sudo aptitude install sysv-rc-conf
and invoke it: