How should a complex single-page JS web application be structured on the client-side? Specifically I\'m curious about how to cleanly structure the application in terms of it
NikaFramework allows you to create single-page application. Also allows you to write HTML, CSS (SASS), JavaScript into separate files and bundle them into only one output file in the end.
I would recommend to explore Yeoman. It allow you to use existing "best practice" for your new project.
For example:
if you decide to use Angular.js, there is a Yeoman generator, that give you a structure for routing, views, services, etc. Also allow you to Test, minify your code, etc.
If you decide to use Backbone, checkout this generator