I've seen a lot of great answers here recently to your question. I would like to comment, however, that I've not yet seen a true Design / Build, Custom Home Builder respond and would like to throw my two cents in.
After working for four small to national home builder in Colorado and building in over 60 communities along with over 10,000 homes, we varied in hard costs from $50/sf up to $200/sf, so again many of the answers below are certainly correct. The one thing you won't see here however is what your unique dream home will cost.
Now have three companies of my own and working the custom home business from the Design / Build aspect, this, in my opinion, is the only way to build a home. It caters to you, the owner, in what you need, can afford and ultimately will enjoy as your home. We, together, can search out the right land, fees, home style / genre, costs, finishes, etc.
First step is "Design" and with the right plans and/or architect we work through the best design that will blend with your lifestyle, while at the same time understanding what the costs are along the way keeping the budget in mind. This includes selecting all of the products, colors and finishes, that you so desire. Also during the stage, there are multiple preliminary budgets that are arrived at to be sure were going down the right path on costs.
Second step is "Build" and with being a one stop, "turnkey" operation, we handle all of this as well, taking the design and costs we came through with on the front end and executing the permitting, land development and building of your new home.
In summary, to answer your question on what are the current costs for building a custom home and as you can tell from the answers you may have already received, there is not one answer. The Deign / Build process, however, will get you the best overall answer and will also give you the best overall breathtaking experience at arriving at your dream custom home.