I hope I'm not bumping this thread unnecessarily, but one thing that the OP never really stated is what sort of situation is he trying to provide security against.
Security against robbery and home invasion?
Security against natural disasters?
Security against the collapse of government (short or long term), society, etc?
I think the first 2 are fairly credible, but if you build a fortress you can become a target. Securing against the third option could eat all of your time and resources. Alternate power sources, gardens, green houses, cisterns, etc, are all great ideas, but these things need regular maintence. If you don't enjoy gardening, and you aren't planning to ride out the fall of society, then a garden, greenhouse, or hydroponic garden would become a chore instead of something to enjoy.
Next thing to ask is what kind of natural disasters you need to ride out? I am on the gulf coast, so hurricanes are at the top of my list, followed by floods, then tornados. If you are in the midwest, you don't need a week's worth of food and water to ride out a tornado. Even still, it would be relatively easy to stock a week's worth of food and water for 2 or more people in a basement provided that you have a schedule to rotate the material out and keep it fresh. An escape tunnel wouldn't be a bad idea if you thought your structure would collapse in a natural disaster AND help wouldn't arrive within a reasonable amount of time.
I do like the idea of a fuel oil supply with a generator plumbed into the supply and wired directly to the house. If you have a decent natural gas supply running to your property, you can buy natural gas generators. Either way I would look into buying enough generator for the whole house and dropping into an outbuilding built with the same construction as the house (reinforced concrete walls and ceiling, etc). Keep in mind that big generators need regular maintence and are pretty expensive. Think $20K or more. If you are going to drop fuel oil or LPG tanks on your property, I would try to hide the tanks as best as possible behind some berms. At least try to hide them as best as possible from the road. This may not be easy or attractive to do, but if you own enough land, you should be able to pull it off.
I like the idea of the upgraded home security features, such as reinforced doors, frames, locks, windows, as well as a safe room. Better yet, a safe room where you can drop a heavy gun safe. Hire a professional for this type of work though to make sure it is done right and to code.
You can rack up a huge bill for this type of build, even into a standard dwelling, and you may not get your money back out of the upgrades if you want/need to sell the house down the line. Remember, this is your home first and foremost. You should be comfortable there as well as safe, and should enjoy living there. If you build in so many features that you end up having to spend all of your time and money maintaining the fortress (and you don't enjoy the maintence and would rather be shooting, hunting, fishing, etc), then you will stop the maintence process and your fortress will be no good to you.
Good luck OP, let us know what you decide to do!