The justification for using JavaScript for server/desktop/mobile applications seems to essentially be that a certain large group of programmers only know JavaScript.
My bet would be that languages specifically designed for the JS ecosystem (whether JS itself or something like CoffeeScript or TypeScript) will continue to be the most popular for writing most of an app, with some apps dropping down to C or C++ or Rust compiled to wasm for a subset of performance-critical code.
I'm sure once webassembly is ready, that'll at least get more popular.
Which is also why I think the emphasis on JS is wrong: the main selling point of these technologies is NOT javascript, is HTML5/ CSS. Javascript is just a (very handy indeed) scripting language like any other: frankly the logic and requirements of most applications around are not complex enough to justify the usage of anything more solid or complicated than that. Just today I was contacted by a former colleague, a Java developer, asking advice on using Electron to develop a quick desktop application.
On the other hand, there is a long list of languages that transpile to javascript. So where are the masses of serious C#/ Java/ <pick-your-language> developers using transpilers to write the logic of their web applications?
I think it is catching on with C++ game developers, who want to be able to run the same codebase natively or in the web browser. The Unity 3D game engine has built-in support for this using WebGL, for example.
I don't know if CLR or JVM languages have been successfully transpiled to the browser using asm.js / WebAssembly (it wouldn't be very efficient at all, so I doubt that will ever be popular).