Concerning the folders you mentioned:
/libs is usually used for custom classes/functions/modules/vendor or /support contains 3rd party libraries (added as git
sub-module when using git as source control)/spec contains specifications for BDD tests./tests contains the unit-tests for an application (using a testing
framework, see
here)
NOTE: both /vendor and /support are deprecated since NPM introduced a clean package management. It's recommended to handle all 3rd-party dependencies using NPM and a package.json file
When building a rather large application, I recommend the following additional folders (especially if you are using some kind of MVC- / ORM-Framework like express or mongoose):
/models contains all your ORM models (called Schemas in mongoose)/views contains your view-templates (using any templating language supported in express)/public contains all static content (images, style-sheets, client-side JavaScript)
/assets/images contains image files/assets/pdf contains static pdf files/css contains style sheets (or compiled output by a css engine)/js contains client side JavaScript
/controllers contain all your express routes, separated by module/area of your application (note: when using the bootstrapping functionality of express, this folder is called /routes)
I got used to organize my projects this way and i think it works out pretty well.
Update for CoffeeScript-based Express applications (using connect-assets):
/app contains your compiled JavaScript/assets/ contains all client-side assets that require compilation
/assets/js contains your client-side CoffeeScript files/assets/css contains all your LESS/Stylus style-sheets
/public/(js|css|img) contains your static files that are not handled by any compilers/src contains all your server-side specific CoffeeScript files/test contains all unit testing scripts (implemented using a testing-framework of your choice)/views contains all your express views (be it jade, ejs or any other templating engine)
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