I believe you're missing the point: with asm.js, JS isn't being used as a "silver bullet", but merely as a kind of "assembly" of web browsers. It's not that we love JS so much, it's that it's pretty much part of every browser, and as such code compiled for asm.js will run in any browser, albeit without any asm.js specific speedup if a given browser does not support it.
Can I run CLR/JVM/Mono in asm.js today? Are there any clear plans for it? Will performance of this scenario equal to that of NaCl? I have my hopes about asm.js but it's good to see that there is an alternative that is evolving in parallel.
You could try compiling Mono/Java to asm.js and see for yourself. Of course performance will not be equal to that of NaCl, but portability will.
I don't see NaCl as a viable alternative, I see it as an attempt of locking down the user to a specific browser, and also as a potential security worry.
The thing is that NaCl lets e.g. game developers use languages and tools _they_ like _today_ to generate great products that run with reasonable performance and are deployable to a decent app-store, here is a poster child: http://www.tested.com/tech/web/3263-how-bastion-can-run-in-a...
You can do the same with Emscripten + asm.js. You don't code in Javascript, you just compile to JS. The products will run with less performance than native, I'm sure, but at least they're not dependent on Google's app store.
And, for me personally if I'm going to run a native app, I see no reason at all to have it run inside a web browser.
