carputer carpc security

A DEI 502T might work (closed loop sensor), it can be triggered when a component is disconnected (run it inline with harness or somewhere they would have to disconnect it to remove.) It won't prevent them from trying, but if they are already in the car and you have an alarm system already, it's probably to late anyways ;)

A heavy gauge security wire attached to it with security screws (need a special tool to undo) would slow them down, but thats all it will do is slow them down a tiny bit, and trying to find a place to attach it to a probably plastic cased electronic part could be fun...

A good alarm system that will keep them away from getting inside would be the best way (shock/glass break/interior motion sensors etc maybe), and hopefully no one will stick around long enough to get inside and tear into the dash. As you said making the system look stock and not stand out, a bit of tinting too would help a bit as they might over look whats inside. Look at a two-way alarm so at least you might get a heads-up if someone messes with the car and can get out there to stop it or call the cops etc...

I'm sure others will come up with some more interesting ideas :)

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The general rule of theft is the harder you make something to remove the more damage that thief is going to do to try and get it out.  I would recomend a strong visual deterrent (like a highly visible flashing LED) and try to make everything look as stock as possible.  Once they are in the car there isn't much you can do to prevent them from either taking everything or causing so much damage that you wish they would have just taken everything and not demolished your entire center console / dash. 

Me, personally, would rather have a theif steal everything and leave me with minimal damage to my vehicle instead of steal nothing, break all the equipment in the process, and leave me with $2500 in repairs to the vehicle from their struggle trying to remove my stuff.