Stocking a retreat is a complex series of tasks that should be done dispassionately. It will be expensive and may take several years, so make your purchases systematically and in strict order of priority.
At present, the only items that I would recommend bumping up in priority would be the private acquisition of your core firearms battery. (One rifle, pistol, and shotgun for each adult family member, and a .22 rimfire rifle for each child.) With talk these days about “closing the gun show loophole” (requiring a paper trail on all gun purchases), this should be one of your top priorities!
Go through your cabinets with clipboard in hand and calculate what you use at home every month. Everything: from envelopes to toothpaste to paper towels to motor oil to teriyaki sauce. Everything! Then do some multiplication, depending on how long you expect to have to hunker down. Then double or triple those numbers, depending on how many extra people are likely to show up at your retreat on TEOTWAWKI+1. And there will almost certainly be newcomers! Just look at the number of people from the Gulf Coast displaced by Hurricane Katrina last week that just drove a thousand miles or more and are ending up on the doorsteps of their relatives. Some of them have very few possessions. I imagine that a future full scale TEOTWAWKI will create dislocations and refugee mass migrations an order of magnitude larger. So be prepared to dispense lots of charity, and be prepared to have a lot of people under your roof.
Keep shelf life in mind. (You can’t store 10 years worth of vitamins, because they won’t store that long unless you buy an ultra-cold medical freezer.) You will soon find that you’ll need a lot of shelving, plus metal mouse-proof lockers for the items that come in paper or plastic packages. Buy your shelving and lockers used, from a surplus office or industrial supply house.
One key reference on stocking your retreat is the book The Alpha Strategy, by John Pugsley. Sadly, this book is long out of print, but it should be available via inter-library loan. Borrow a copy and make yourself photocopies of the most important sections.