This also depends very much on which Unix variant you are using. On a Linux system, it also depends on your distribution! For example, HP-UX 9, HP-UX 10.20, Slackware Linux, Redhat Linux all have their own quirks... The two HP-UX variants do it differently (changed in version), and the Linux variants do it differently (one uses a more BSD rc and the other uses SYSV style...).
So... The whole point of this is to please post all you can about your system!
All scripts and links are executed from the /etc/rc[n].d/ directories. Many of these may be files located in these locations or links to files or scripts in /etc/init.d/. Usually you can stop and start any service (if the script allows) by issuing a request from the command line.
# /etc/rc2.d/S80sshd stop
... as an example, to stop the SSH daemon.
If the file begins with an 'S' then it is utilised when the system comes up, if it starts with a 'K' it stops processes when the system goes down.
We disable these scripts by renaming them with lowercase 's' and 'k' - this way they are never run whenthe machine comes up.