Java applets and JWS applications will always have their place IMHO. While it’s true that the advent of HTML5 with its Canvas and WebGL capabilities means that many of the things that were once only possible with Flash or Java will now be possible without any browser plug-in, there are still going to be situations where you need a fully-fledged programming language like Java inside the browser. Using pure JavaScript is simply not an option if you have libraries of code in any other language (Java, C++ etc.) that you want to use in a client-side application/applet. Yes, you will be able to do a lot with HTML5 but re-using existing code is not one of them. Besides, JavaScript is not exactly the “best” programming language out there now is it? And it doesn’t equip the developer with the enormous range of “free” functionality that comes with the Java Platform.
Java applets and JWS applications may not be the ideal deployment solution for mainstream consumer-oriented software and content but they will still be the most appropriate technologies in many future scenarios.