The first thing is to get inspired and there's nothing like heading to your nearest library and grabbing whatever you can find on the latest designs. You should be able to take a whole variety of books and magazine that will help you articulate your vision of dream home. They have tittles on building eco homes, natural homes, tatami room specialties, homes under 100 meter square,etc..
Experts mention you need to do this as a first step before going out to look for land. But I like to keep an open mind and did this in parallel. Great designs will make some of the irregular shapes of land efficient and cozy. So it's good to know what's out there.
The HOW-TO books.
The first book on the left-hand side is a great resource for getting a good knowledge foundation on building a home and the numerous options open to you. There's also a special section on how to build a "Low-Cost" home.
The second book is half explanation, half list of check boxes and takes a methodical approach.
The check lists are great for pointing out the little details that are easily forgotten (number of light switches, or electrical outlets, etc).
So above 2 are great for the general plan of the house. But in reality some of your appliances will dictate the more detailed plan. For example if you want an American Gas-vented dryer (as opposed to the Japanese dryers that just heat your clothes), you'll need to build the air ducts and ensure the counters are wide enough. If you're a gadget fan like I am, it's great browsing some of the latest technologies in the kitchen. MSRP (Manufacturer Suggested Retail Price) are listed for almost all items. In general expect a 30% discount on those prices as your builder will buy direct.
Typically, the larger you buy the larger the discount.