Minecraft is a great example of what can be accomplished in a browser, and it's written in Java, not JS. I doubt if it is even possible/practical to attempt such a complex project in JS.
Java is clearly a more powerful platform, and it probably runs significantly faster (this is just my guess, though). About the only drawback of Java I can think of is that it runs as a plugin, and with the trend towards plugin-free browsers (e.g. IE10 metro) Java applets may become obsolete in mobile environments. This has already happened with Flash on iOS.
What do you think? Is there a future in developing Java-based Web apps (especially for mobile devices)?