Adding other javascript to it's own variable, and getting Drupal to aggregate it nicely on cache refresh.

html.tpl.php

<?php print $footer_js; ?>

pilsner.module

<?php

function pilsner_init() {

  $theme_path = drupal_get_path('theme', 'pilsner');
	
	$js_files = array(
	   'libs/jquery.js',
	   'libs/handlebars.js',
	   'libs/jquery.easing.js',
	   'libs/jquery.infinitescroll.js',
	   'libs/jquery.mousewheel.js',
	   'libs/jquery.validate.min.js',
	   'libs/jquery.flexslider.js',
	   'libs/swfobject.js',
	   'nation/Utils.js',
	   'nation/EventDispatcher.js',
	   'nation/VerticalScrollbar.js',
	   'pilsner/website/models/global/WebsiteEvents.js',
	   'pilsner/website/views/HeaderView.js',
	   'pilsner/website/views/ArticleView.js',
	   'pilsner/website/views/ContentGridView.js',
	   'pilsner/website/views/AgeGateView.js',
	   'pilsner/website/views/FormView.js',
	   'pilsner/website/views/TermsView.js',
	   'pilsner/website/views/common/ExpandingList.js',
	   'pilsner/website/views/common/ExpandingContent.js',
	   'pilsner/website/views/common/Dropdown.js',
	   'pilsner/website/views/common/YouTubeVideoPlayer.js',
	   'pilsner/js/libs/googlemaps.infobox.js',
	   'pilsner/website/controllers/MainController.js'
	);
	
	foreach($js_files as $j) {
   	drupal_add_js($theme_path.'/js/'.$j, array('type' => 'file', 'scope' => 'footer_js', 'preprocess' => true));
	}

template.php

<?php

function pilsner_preprocess_html(&$variables) {

   $variables['footer_js'] = drupal_get_js($scope = 'footer_js');