Folder structure for both server side and thick client web app

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/

Just put the whole /webapp under /public so you'll end creating, for instance, frontend's models under /public/webapp/models

appname  |--models  |  |--appmodel.js  |--public  |  |  |--webapp // extjs/backbone files  |  |  |  |--models  |  |  |  |--controllers  |  |  |  |--css  |  |  |  |--js  |  |  |  |--img  |  |  |  |--views  |  |  |  |  |--appview.ejs  |  |  |  |  |--extbasedview.ejs  |--routes  |  |--router.js  |--app.js

Heres my suggested folder structure:

appname  |--webapp  |  |--img  |  |--js  |  |  |--controllers  |  |  |  |--controller.js  |  |  |--something.js  |  |--css  |  |--views  |  |  |-- appview.ejs  |  |--index  |  |--404 etc.  |--app.js  |--package.json  |--README  |-- etc.

I think its very tidy and easy to navigate in, because all the server and node_modules stuff is outside and the files I need for the application is in the "webapp" folder. If you really need a folder called "public" (I cant remember if express needs one or not) I think you can just rename the "webapp" folder to "public", or drop the "webapp" folder inside "public". I would also recommend using AngularJS instead of .ejs, but do what you want to do. :)