I'm building a web application using a MEAN stack: MongoDB, Express, Angular, and Node.js, based on Daftmonk's angular-fullstack Yeoman generator.
My preferred IDE is IntelliJ IDEA, partly because I also work on Ruby/Rails, Java, etc., and partly because it's f#%ing bad&@s and I love it.
What's the best way to configure it for this project?
Here's the best I've been able to do so far.
There are some crucial IntelliJ plugins to install:
As a peace offering to the mighty IntelliJ, use Java as project SDK:

I prefer to configure four separate modules, to help separate back-end vs. front-end JavaScript dependencies:

Add the bower_components library to the client module, and the node_modules library to the server module:

And be sure to enable JavaScript libraries in the editor.

Per best practices, we do not commit the local IntelliJ IDEA configuration folder (/.idea/) to the repository, instead adding it to the .gitignore file like so:
# IntelliJ IDEA local workspace
.idea
However, for some developers' convenience (and others' dismay) we do commit the four IntelliJ module .iml files to the repository:
client.iml
server.iml
e2e.iml
doc.iml
Happy coding!