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JavaScript is an OO type interpreted language that runs on the clients browser, enabling interaction between the user and the document, without the need to always go back to the server for processing. for example to validate form input. There is no reason why you would want to stop JavaScript from executing on your browser, unless yet another security hole is found in the browser that allows data to be captured by a third party. All the *known* security holes have been plugged.
Java is a byte compiled language that is a fully fledged OO language. It again runs on the clients browser. It can do things that JavaScript cannot do, like reading a file on the same server that the document was served from (I believe this is correct). It can do graphcs. I'm not too sure if there are valid reasons why you would not want to allow Java to execute on your browser, other than that Java applets can be quite big and can take a while to download. The initial loading of Java in the browser can take quite a few seconds to start up.