They're essentially the same... They both use swig for templating, they both use karma and mocha for tests, passport integration, nodemon, etc.

Why so similar? Mean.js is a fork of Mean.io and both initiatives were started by the same guy... Mean.io is now under the umbrella of the company Linnovate and looks like the guy (Amos Haviv) stopped his collaboration with this company and started Mean.js. You can read more about the reasons here.

Now... main (or little) differences you can see right now are:





SCAFFOLDING AND BOILERPLATE GENERATION

Mean.io uses a custom cli tool named 'mean'

Mean.js uses Yeoman Generators



MODULARITY

Mean.io uses a more self-contained node packages modularity with client and server files inside the modules.

Mean.js uses modules just in the front-end (for angular), and connects them with Express. Although they were working on vertical modules as well...



BUILD SYSTEM

Mean.io has recently moved to gulp

Mean.js uses grunt



DEPLOYMENT

Both have Dockerfiles in their respective repos, and Mean.io has one-click install on Google Compute Engine, while Mean.js can also be deployed with one-click install on Digital Ocean.



DOCUMENTATION

Mean.io has ok docs

Mean.js has AWESOME docs



COMMUNITY

Mean.io has a bigger community since it was the original boilerplate

Mean.js has less momentum but steady growth



On a personal level, I like more the philosophy and openness of MeanJS and more the traction and modules/packages approach of MeanIO. Both are nice, and you'll end probably modifying them, so you can't really go wrong picking one or the other. Just take them as starting point and as a learning exercise.





ALTERNATIVE “MEAN” SOLUTIONS

MEAN is a generic way (coined by Valeri Karpov) to describe a boilerplate/framework that takes "Mongo + Express + Angular + Node" as the base of the stack. You can find frameworks with this stack that use other denomination, some of them really good for RAD (Rapid Application Development) and building SPAs. Eg:

You also have Hackathon Starter. It doesn't have A of MEAN (it is 'MEN'), but it rocks..

Have fun!