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
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
PHP has DOMDocument for navigating the DOM. I haven't heard of anything for executing JavaScript.
For Java, be sure to check out HtmlUnit and HttpUnit.
Start from this post and follow a links. Or just search for Rhino.
node.js ?
Node can run any javascript file in its console. I would try node first & see if it can do what you want as it likely has the largest user base & documentation.
There are now several projects that do a really good job of this:
PhantomJS is a headless version of WebKit, and there are some helpful wrappers such as CasperJS.
Zombie.js which is a wrapper over jsdom written in Javascript (Node.js).
You need to write JavaScript code to interact with both of these projects. I like Zombie.js better so far, since it is easier to set up, and you can use any Node.js/npm modules in your code.