something like this:
...
<body>
<div id="jsNotify"><p>This page works best with JavaScript</p></div>
<script type="text/javascript">
var elm = document.getElementById("jsNotify");
elm.parentNode.removeChild(elm);
</script>
...
This will add the notification at the top of the page, but will remove it if you have JavaScript enabled.
I'm not sure how you can force search engines to dismiss the text inside it. But if you have links, then you can use nofollow to stop the search engine from following the link, like so:
<a href="http://www.example.com/" rel="nofollow">limited site</a>