The manual isn't very helpful in this case, it is even misleading, because \JavaScript command isn't defined by default, only when javascript option is used it is defined. But it is quite easy to define your own version:
\Preamble{xhtml}
\begin{document}
\ScriptCommand{\JavaScript}{\HCode{\Hnewline<script type="text/javascript">\Hnewline}}{\HCode{\Hnewline</script>\Hnewline}}
\JavaScript
var _gaq = _gaq || [];
var pluginUrl =
'//www.google-analytics.com/plugins/ga/inpage_linkid.js';
_gaq.push(['_require', 'inpage_linkid', pluginUrl]);
_gaq.push(['_setAccount', 'UA-45193039-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
\EndJavaScript
\EndPreamble
In this configuration file, \JavaScript command is defined first:
\ScriptCommand{\JavaScript}{\HCode{\Hnewline<script type="text/javascript">\Hnewline}}{\HCode{\Hnewline</script>\Hnewline}}
The \Hnewline commands are used to insert line breaks. The JavaScript code is then inserted without <script ...> tags, because \JavaScript command will take care of this.
One important thing is to place the JavaScript after \begin{document} in the configuration file, this ensures that it is inserted in the HTML header:
<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!--http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd-->
<html xmlns="http://www.w3.org/1999/xhtml"
>
<head>
<script type="text/javascript">
var _gaq = _gaq || [];
var pluginUrl =
'//www.google-analytics.com/plugins/ga/inpage_linkid.js';
_gaq.push(['_require', 'inpage_linkid', pluginUrl]);
_gaq.push(['_setAccount', 'UA-45193039-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<title>mytitle</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="TeX4ht (http://www.tug.org/tex4ht/)" />
<meta name="originator" content="TeX4ht (http://www.tug.org/tex4ht/)" />
<!-- charset=utf-8,html,xhtml -->
<meta name="src" content="sample.tex" />
<link rel="stylesheet" type="text/css" href="sample.css" />
</head><body
>
