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
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.