How to Calculate Total Cost of Building a House?

Recently, I have been considering the total cost to build a house, and quite honestly I thought this would be a little easier to understand than it has proven to be. Depending on land, material, labour, and a whole list of not so planned extras like permits and finishing work, these costs just keep climbing. I have read that they best construction takeoff services comes in handy to help provide material quantities and material pricing before a build, but I have some doubt that they will actually help in practice. My question to those of you that have built your homes in the past is; how did you initially cost it? Did you use software, do you rely on a contractor quote or an extensive material takeoff? Alternatively how did your initial numbers compare to what you ultimately paid. I would love to hear your experiences or tips you have to help stick to the budget.