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 s
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.
Have you tried Bringing the Browser to the Server?
PhantomJS does this and can be used with any server side language. See some integration modules below for NodeJS and PHP
NodeJS
https://npmjs.org/package/node-phantom
https://github.com/sgentle/phantomjs-node
PHP
https://github.com/diggin/php-PhantomjsRunner