We just went through a whole lockdown and restore process for our Joomla process and I just scanned our code with a google fetch through webmaster tools and here is what I am seeing in the head of my homepage:

HTTP/1.1 200 OK
Date: Thu, 20 Jun 2013 18:00:32 GMT
Server: Apache
X-Powered-By: PHP/5.3.22
Content-Length: 32948
Connection: close
Content-Type: text/html

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en-gb" lang="en-gb" >
<head>
<script src="http://www.massalfa.org/Assets/JS/JQuery/JQuery.js" type="text/javascript"></script>
<base href="http://www.massalfa.org/" />
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="robots" content="index, follow" />
<meta name="keywords" content="Viagra, Assisted Living, Viagra Massachusetts Assisted Living, MA Assisted Living, Elder Care, Elderly Living Space, Assisted Living Facility" />
<meta name="googlebot" content="NOODP">
<meta name="robots" content="NOODP">
<meta name="robots" content="noydir">


<meta name="generator" content="Joomla! 1.5 - Open Source Content Management" />
<title>Buy Viagra (Sildenafil) Online >> Lowest Prices Guaranteed</title>
<meta name="description" content="Buy Viagra online from an official certified pharmacy, OVERNIGHT Shipping, Exclusive & competitive discount prices, express shipping & discrete packaging." />

<link href="/index.php?format=feed&type=rss" rel="alternate" type="application/rss+xml" title="RSS 2.0" />
<link href="/index.php?format=feed&type=atom" rel="alternate" type="application/atom+xml" title="Atom 1.0" />

<script src="/js/OrganizationTabbedPanels.js" type="text/javascript"></script>
<link href="/css/HomeTabbedPanels.css" rel="stylesheet" type="text/css" />
<link href="http://www.massalfa.org/css/MA-Global.css" rel="stylesheet" type="text/css" />
<link href="http://www.massalfa.org/css/MA-Home.css" rel="stylesheet" type="text/css" />
<link href="http://www.massalfa.org/Assets/JS/JQuery/ToolTip/ToolTip.css" rel="stylesheet" type="text/css" />
<script src="http://www.massalfa.org/Assets/JS/JQuery/ToolTip/ToolTip.js" type="text/javascript"></script>
<script src="http://www.massalfa.org/Assets/JS/JQuery/Dimensions.js" type="text/javascript"></script>
<!--[if !IE]><!-->
<link href="http://www.massalfa.org/css/IE.css" rel="stylesheet" type="text/css" />
<!--<![endif]-->
<meta name="google-site-verification" content="5WL6fE3YT8bIgX0df-pHuCErWVZCwCT42Rud7DbwWDQ" />
<meta name="msvalidate.01" content="F44FFAFB7669C57DD48ABA7337805334" />
<script type="text/javascript">
function ClearFields(Item) {
Parent = $(Item).parent().parent().parent().parent().parent();
Checkboxes = $(Parent).find('input:checkbox');
$(Checkboxes).each(function() {
$(this).removeAttr('checked');
});
Text = $(Parent).find('input:text');
$(Text).each(function() {
$(this).val('');
});
Select = $(Parent).find('select');
$(Select).each(function() {
//console.log($(this));
$(this).val('');
});
}
</script>
</head>

Has anyone ever dealt with anything like this on their joomla sites and how did you fix it?