Best Way to Include Scripts on a Specific Template Page

The following (in your theme’s functions.php) will register your script, and set jQuery as a dependency. So when you enqueue it, jQuery will also be enqueued.

function my_scripts_method() {
   // register your script location, dependencies and version
   wp_register_script('my_custom_script',
       get_template_directory_uri() . '/js/custom_script.js',
       array('jquery'),
       '1.0' );

}
add_action('wp_enqueue_scripts', 'my_scripts_method');

You can then enqueue your script one of two ways. In your theme’s functions.php you can use the template_include filter the get the template being used using is_page_template()

add_filter( 'template_include', 'my_load_script_for_template', 1000 );
function my_load_script_for_template( $template ){
     if(is_page_template('my-template.php'))
        wp_enqueue_script('my_custom_script');

return $template;
}

Alternatively, if you are using 3.3+ and your theme calls wp_footer() then you can just call wp_enqueue_script('my_custom_script') inside the actual template page.