You can pre-render the whole (big) section of the site and then use some JS mapper/loader to dynamically load scripts and execute custom code.
You could create jQuery plugins to handle different parts of your functionality and load them when needed. On JS Loaders there is a whole section over at jster.net For routing you could use something like the Davis Mapper.
It would be preferable to have the JS resources static where possible and handle the dynamic content via AJAX calls to the server side. Hope this helped. :)