This is simple alter function I had to write while addressing an issue on the DrupalCon site. It led to this blog post. http://pixel-whip.com/blog/12/03/all-cool-kids-back-bus

template.php

<?php

/**
 * Implements hook_js_alter() 
 */
function shizzle_js_alter(&$javascript) {
  // Collect the scripts we want in to remain in the header scope.
  $header_scripts = array(
    'sites/all/libraries/modernizr/modernizr.min.js',
  );

  // Change the default scope of all other scripts to footer.
  // We assume if the script is scoped to header it was done so by default.
  foreach ($javascript as $key => &$script) {
    if ($script['scope'] == 'header' && !in_array($script['data'], $header_scripts)) {
      $script['scope'] = 'footer';
    }
  }
}