Is the type of architecture something that local builders have experience with? Are the materials used similar? For instance, Texas has a lot of full brick homes, while the Southeast has a lot more vinyl or hardiboard homes. Are you looking for a one or two story home? A one story is more expensive per square foot, because more foundation and roof are needed, which are major contributors to the cost of the home. Are you looking for a very large kitchen with granite countertops, or a more typical 10x10 kitchen with a nice Formica countertop? There can be a large variance in finishes - tile vs. vinyl in bathrooms, two-piece crown molding vs no crown molding, etc.
Also, by square foot cost, are you including the cost of land, or are you planning to purchase a piece of land? If so, find out whether the builder is including septic/well or city water/sewer hookups, permits, and land clearing/preparation in the cost per square foot.
Hope this helps as you start your search!