Is there any programming libraries available that will parse an HTML document, execute JavaScript and then allow me to navigate the DOM? This needs to be performed server side, not client side. Any language will do, but Java, PHP, or Ruby are preferred.
PHP has DOMDocument for navigating the DOM. I haven't heard of anything for executing JavaScript.
Java has support for javascript with Rhino, also look at this page for server side javascript solutions: http://en.wikipedia.org/wiki/Server-side_JavaScript
in java: http://lobobrowser.org/cobra/java-html-parser.jsp
this is a a Javascript-aware, CSS-aware HTML parser
the most important feature in relation to your question: It is Javascript-aware. DOM modifications that occur during parsing will be reflected in the resulting DOM.
You should look at the Aptana Jaxer Server side javascript implementation, you can run any javascript and perform DOM manipulation in server side as you did in client side .It simply supports all JS libraries include JQuery, Mootools,etc in a server side.