Inside of a given area (like your city or county) it's almost all based on location.
Comparing, say, Florida to Kentucky, it's location plus cost of building. The cost of building in one area could be different from another for a variety of reasons. For instance, in some areas you'd have primarily wood houses, others primarily masonry. You'll also have different building codes and regulations (IE Florida your houses have to be reasonably hurricane resistant). You'll also have local materials (live near a good source of lumber?) that may contribute a good bit to the cost of a house.
I'd imagine though that even if the houses were 100% identical, you'd still have differences in labor and materials costs no matter what. Ballpark I'd guess that you could see anywhere from a 10-25% cost increase just to build the exact same house. (prob 10% deviation in materials, another 10-20% in labor costs). Edit: Note that I'm talking about the price of the HOUSE not the price of the whole package. When you have a house appriased, they give you a land value and a house value. Just for refernece, my 1100 sqft concrete house in florida just appraised at $90k for the house and $110k for the 1/4 acre of land it is sitting on. Given the current rate of property appreciation, in a few years I can expect the house to still appraise for ~$90k, but the land will probably appraise at $120k-130k. The $90k is basically the "replacement" cost of the house, or what it would take to build a new one if it was destroyed.