Currently I am using Node.js for the backend and either extjs or backbone for the client and I am now completely confused on the folder structure.
Using express
In your place, I would do that way:
appname
|--ServerCode
| |--controllers
| |--models
| | |--appmodel.js
| |--routes
| | |--router.js
| |--views
| | |--appview.ejs
| |--app.js
|--public
| |--css
| |--js // any client-side javascripts
| |--models
| |--controllers
| |--...
The main idea is to place public folder outside of the scope of your server javascript files.
See an example here: https://github.com/madhums/node-express-mongoose-demo/