Depends on the level on finish and amenities that you want, whether you want to match the neighborhood, and whether there are any special considerations.
For example, if you demand a huge kitchen with two prep sinks, a range and a built in double oven, you will pay a lot more, as that will require more electrical, structural, and plumbing. Also, number of bathrooms (especially the full variety), is more important than the actual square footage of the property.
If you live in a high rent area (Corona del Mar, Newport, etc) the expectation is that you will have the above, as well as high end tile work, high-end floors, etc. Come resale, you need to have paid for it, or your resale price will be less.
if you are looking at an area that is difficult. you will pay. For example, if you have seismic considerations (Laguna Beach, you know who you are), you can spend $85k to $200K for footings.
Now, can you make some of this work for you? Yes.
My wife and I toured a new home (whose order had been canceled) around Christmas. Due to the fact that the order had canceled before the tile went in the bathrooms, the builder wanted to keep the cost of the tile work close to the bone. The builders designer picked off white (kind of a nice cream) matte Dal-Tile, and using standard Dal-Tile fittings (edgeing, corners, etc.) put together a very nice piece of work. In one shower, they had a 4"x4" field, with a 36" x 36" inset, edged, of 6"x6" rotated 45 degrees, all un standard Dal-Tile.
You can also repurpose cabinet carcasses, from one structure to another, as well as windows and doors.
If you need the type of footings desribed above, for a nominal price increase, you can have a full basement, and increase your total square footage.
I would expect that you can build for about $250 to $350 per square foot.
If you would like some ideas on maximizing value per square foot, may I recommend "A Not So Small House" ?