If you need to protect the software, then make sure you include some "failsafe" code so that the gadget will lock up and not be functional outside of its normal environment. For example, have some of the code in eprom and overwrite it as part of the kill process.
If you need to protect the hardware from being discovered and duplicated, then you may want a means for physical self-destruction as a last resort (doomsday scenario). A few creative lines of code would probably do the trick.
As mentioned above, you can't prevent reverse engineering but you can at least make it somewhat difficult and time consuming.