<?php
  function MYTHEME_preprocess_html(&$variables) {
    drupal_add_js(drupal_get_path('theme', 'MYTHEME') .'/script.js', 'file');
  }

<?php
drupal_add_js(path_to_theme().'/js/script.js');

<script type="text/javascript" src="path/to/file/scripts.js"></script>