Everything else is pretty developer specific in my opinion. I'd recommend Visual Studio Code for a text editor (if you don't already have a preference). It has built-in git integration and installing new plugins is trivial.
It's pretty easy to break it down to the common parts but there definitely is quite a bit to learn.
NodeJS or Python or Ruby
These are your fairly standard backend choices. They all have minimalist and full featured frameworks for building applications including but not limited to Express, Koa, Ruby On Rails, Sinatra, Django, Flask. Go is also fairly easy to get going quickly in. There is not really a wrong choice here for a personal project.
In the case that you want a single page application that works with the backend you made with the previous choices:
Backbone or Angular or React+Redux(any flux implementation will do)
These are for consuming your backend and any of them will do. Learning Angular is its own thing despite it being javascript. React+Redux seems a little odd by embedding html in your javascript but once you get the hang of it it's pretty neat. Don't know much about Backbone but I've heard its fairly easy to use.
Bootstrap is pretty easy to learn and use to make your website responsive with minimal effort.
Heroku is by far the easiest platform for deployment and horizontal scaling however it can get pricey quickly. AWS has a similar solution with Elastic Beanstalk but I've got no experience to share with that. If you want all the control (but more work) you can go with Digital Ocean for a 5$ VPS. Unlike Heroku you will have do all admin work like installing necessary packages, databases, and configuring a web-server but you can control every little bit of your application without having to spend more than $5 a month.
Three.js is just for rendering. Goo Engine is a complete game engine with support for rendering, physics, 3d audio, scripting, state machines, timeline... And there's also Goo Create which makes it super easy even for non-coders to build a scene that can be loaded into the engine.
I'm not sure how to compare extensibility in this case, but both are indeed extensible: For Three.js you might want to add a new class, for Goo you might want to add a new type of component for your entities.
