It depends on your request. For instance, lastly, I had been removed all Prototype scripts from the Homepage
of the Magento store which I didn't face any problem. But as I said, it depends on your theme, extensions etc.
To moving the script :
Find the following line in page.xml
of your theme
<block type="core/text_list" name="before_body_end" as="before_body_end" translate="label">
And insert the following just before :
<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
<action method="addJs"><script>your_script.js</script></action>
</block>
For Magento 1.9 use this:
<block type="page/html_head" name="jsfooter" as="jsfooter" template="page/html/jsfooter.phtml">
<action method="addItem"><type>skin_js</type><name>js/yourskinfile.js</name><params/></action>
</block>
Create the template file in app/design/frontend/[package]/[theme]/template/page/html/jsfooter.phtml and put the following
<?php echo $this->getCssJsHtml() ?>
Add below in your template just before closing </body>
tag.
<?php echo $this->getChildHtml('jsfooter') ?>
If you are using a core/text
block include the full text you want printed inside the text
tag
<reference name="head">
<block type="core/text" name="shim">
<action method="setText"><text><![CDATA[<!--[if lt IE 9]><script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script><![endif]-->]]></text>
</action>
</block>
</reference>
Best Answer
You can't natively you must use a third party Module, you can try this
http://inchoo.net/magento/how-to-add-external-javascript-css-file-to-magento/