Running a script at boot is sometimes very important. You, the user, can decide which programs run on log in to your account via the "start up applications" system menu.
However this doesn't do system wide scripts. A good example of one that would be an important system wide script is a firewall script.
To get this to run as linux boots up, copy the script to /etc/init.d/.
Then, run the command
update-rc.d <script file > defaults
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