The correct way of doing this is to do a document.write of the tag based off the current hostname:
Correct:
<script type="text/javascript">
document.write("<base href="http://" + document.location.host + "" />");
</script>
This method has produced correct results in IE, FF, Chrome, and Safari. It produces a (correct) different result than doing the following:
Incorrect:
<script type="text/javascript">
var newBase = document.createElement("base");
newBase.setAttribute("href", document.location.hostname);
document.getElementsByTagName("head")[0].appendChild(newBase);
</script>