Omega Subthemes, Modernizr, and Javascript placement
I have now done a few Omega based sites, and have some answers about these.

I have not run into any problems with moving the print $scripts to righe before the  closing &lt;/body&gt; in html.tpl.php.  That said, this question on SO has a good discussion on wht this may be outdates advice.

I have also had good results replacing the HTML5 shiv in html.tpl.php with

&lt;?php if ($modernizr): ?&gt;
&lt;script src="&lt;?php print $modernizr; ?&gt;"&gt;&lt;/script&gt;
&lt;?php else: ?&gt;
&lt;!--[if lt IE 9]&gt;&lt;script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"&gt;&lt;/script&gt;&lt;![endif]--&gt;
&lt;?php endif; ?&gt;


and using this in a template_process_html

if (theme_get_setting('mytheme_use_modernizr')) {
  $vars["modernizr"] = "/" . path_to_theme() . "/js/modernizr-2.0.6-min.js";
}


and then wiring up a custom theme variable in theme-settings.php

$form['mytheme'] = array(
    '#type'          =&gt; 'fieldset',
    '#title'         =&gt; t('mytheme settings'),
);

$form['mytheme']['mytheme_use_modernizr'] = array(
    '#type' =&gt; 'checkbox', 
    '#title' =&gt; t('Use Modernizer instead of HTML5 Shiv?'), 
    '#default_value' =&gt; theme_get_setting('mytheme_use_modernizr'), 
);