From the development side of things, I really like Invision. It allows the designer to include user interactions to their designs, which makes it that much easier for the developer to implement things. We use this at my company, and it has been extremely helpful and allowed everyone to be on the same page about how a view should look and function; I cannot stress enough how nice it is to be able to show user flows and interaction in the mockups.

For the MEAN stack, if you are comfortable with javascript I use this repo for prototyping:

github.com/cleechtech/mean-starter

I will clone that and that gives me a server and an angular frontend that is all connected to mongodb with the ability to configure dev environments. It is not even that much started code either.

For authentication with JWT and MEAN I use: github.com/cleechtech/node-jwt-intro

Also most recently I have been using laravel 5 to build web apps quickly. There is a learning curve but in the long run will definitely pay off. If you need help getting started with the framework I wrote an installation guide on medium: medium.com/@connorleech/get-started-with-laravel-…

For me it's simple. I'm best prototyping using good 'ole html, css, and js. I can quickly work through functionality and UX issues that may come up before getting it ready for production.

It all depends on what you are looking to do. Since you mention prototyping in your description I am going to assume that this isn't something that you mean to maintain long term. I would recommend Meteor.js since its got everything you need including a database and http server. It allows you to build it once and run on all platforms (you can generate iOS and Android apps via its cli tools for instance). ReactJS is another good example although I find that that has a larger overhead in getting a project set up (since its just the UI component you are on the hook to set up a lot of the plumbing). Of the two ReactJS is more scaleable but again, if you just want to get going as fast as possible with as much functionality ready to go, MeteorJS is your jam.

I usually create prototypes with proto.io

it's quick and easy, not so useful for website layouts but pretty awesome for app prototypes.