I have some non-trivial computational code that need to be applied on data already downloaded into the browser DOM and captured from user interactions. I do not wish to expose this code. I am wondering if:
I thinks the biggest disadvantage of applet is that it assumes you have a JRE installed on a client machine. Is it really a viable assumption? Of course you can offer to download and install JRE as well, but why bother doing all this only for making some computation? Another question I would ask myself, can your clients be mobile phones, tablets and so on? If so, maybe the Java Script is a better option to go.
And yet another 5 cents :) You mentioned 'opened to eye java script' You should understand that the only real way of protecting your computation code is putting the computation on server. I mean, that even if you have a compiled binary code, java's assembly is easy-to-understand for skilled attacker. And obfuscation that you mentioned (its obfuscation, not signing jar) makes it slightly harder but still not impossible.
The only concern I see here is that if you have a lot of clients that are running the computation simultaneously and you put the burden of computation on your server it can collapse eventually.
Just my thoughts, hopefully this will help you to chose the best direction here...