Because your question is very broad, I am going to give you an outline. Each of these points can be further researched individually.
There are many things you can do that cost no more than any other house and some things that might cost more up front, but save you money in the long run.
Site.Find a site that gives a good Southern exposure on the long axis, so you can take advantage of passive heating techniques. A well designed passive solar house can reduce your heating bill significantly.
Team Players.Architect, mechanical, structural, civil engineers, landscape architect. Do not underestimate the value of a good team of professionals. They may be more of an upfront cost than you expect, but their expertise can be the difference between a successfully sustainable house and a failure.
Materials. Vet your materials: Do they have recycled content? Are they manufactured locally? Are they nontoxic? Are they durable? Quiz the manufacturers and suppliers.
Indoor Air Quality. Use zero VOC compounds and paints at the least. They are easily available.
Heating and Cooling. Besides finding a site with natural heating potential, be sure you build a tight house with more insulation than you think you need, avoiding thermal leaks and bridges. Building a highly efficient building envelope with the best windows you can afford will save you money in the long run. Use a heating unit with a seer minimum of 12 and preferably closer to 17.
Ventilation. With a tight house ventilation is extremely important. Have both natural and mechanical ventilation as part of your design makeup.
Advanced framing techniques.Use advanced framing techniques. This will results in using less wood and having better insulation. Advanced framing techniques can save you money in lumber costs.
Moisture Control. Moisture control is a combination of building science and common sense. First your site drainage should be designed to keep moisture from the house. Waterproofing in your roof and walls is, of course, obvious, but what often isn't obvious is the detailing that avoids condensation traps, "sweating," and other moisture problems. A sustainable house is firstly a well built house, durable, strong and dry.
Daylighting.Natural lighting in the right places improves your quality of life and saves on your electrical bill.
Landscaping.Use deciduous trees strategically for summer cooling. Do not plant within two feet of the house, so soil doesn't build up against the foundation.