This is something that I have put a lot of thought into and what I came up with is the bigger the area you try to make impervious, your costs increase exponentially and in the long run make yourself more vulnerable because you will draw more attention, and have to adapt your defense strategy to cover a larger area. You can fit everything that is truly important into one room if it is organized. For example, if there are 60+ people wandering through looking for supplies, hopefully your house appears to have no supplies and you can sit quietly in your safe room until they pass. If they are starving and in a big enough gang they will find a way in eventually so you don't want your house to be a beacon.

My idea is to build a regular house with a couple exceptions. Hardened steel beneath windows and either inside door, or steel plate able to be quickly hung on the door. Also put a steel plate next to the door on either side that goes up to waist height. Then use secure materials (security doors, security windows) to prevent quick and easy access to the house. The idea being that you will be able to see and identify a threat before it has an opportunity to enter the house, mount a formidable defense then if need be retreat to a safe room.

I personally think that having a safe-room under the footprint of the house is the best idea. Metal detectors are able to mark the re-bar in concrete so if it is outside the footprint of your house an angry mob might not find it, but .gov easily could. My ideal safe-room is just a bunker that has its own hepa-filtered ventilation and two entrances, one being from the house, the other being a defensible hidden exit away from the house. Hidden pill box if you will. Then have your well supply pass through this room before anything else, and have a manual pump tap in there.

This sets a small portion of your house up to protect you for extended periods of time. This leaves the rest of your house open to looters, but it will look just like every other Joe Schmo's house and if the situation is that severe, you won't be running your big-screen TV any time soon anyway. I think that it is important to have a house that will not attract attention like a big tower or barbwire perimeter fence. If nothing else the people that are attacking you will know that they need to be more prepared. This frees up the expense of building a fortress and allows you to buy supplies for longevity and training for you and your loved ones who will be staying with you.

Another thing that I have thought about would be a hidden closed circuit monitoring system that could be battery powered from inside the room so that you could accurately asses the situation in the event of an invasion. You could rig it up to where the batteries would last a long long time, and assuming that you would only use it intermittently during a crisis situation it would last through the worst of the worst.

I would love to have one of those fortress houses that were linked to earlier, but the cost of that would be more than I would care to pay. From a practical standpoint it makes sense to make a safe point to survive in, but if you never need it it would really suck to invest your entire life budget to build it. There is a fine balance between preparing and living a comfortable life, and making preparing your entire life.