Using PHP
The function drupal_add_js() lets you add a reference to a file, as well as inline javascript code:
drupal_add_js('misc/myscript.js');
drupal_add_js('jQuery(document).ready(function () { alert("Hello!"); });', 'inline');
See the function reference page for additional examples and settings.
On a Theme
If found, Drupal automatically includes the file called script.js in the theme directory.
You can also add a js file to the .INFO file using this line:
scripts[] = myscript.js
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