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If you are worried about the end user reverse engineering your application, don't distribute it. If you allow members of the public to get the bytecodes, it can be reverse engineered - even if it is obfuscated, encrypted and packed in an (huck, ptui..) EXE.
As an aside. A deployment technology that works on Windows, Mac & *nix is [Java Web Start|http://java.sun.com/javase/technologies/desktop/javawebstart/index.jsp]. JWS is free and is provided and supported by the makers of the language.