The September 2007 South Region issue of Log Home Living focuses on green building, and there is interesting furniture recycled from old wood, including barn siding, fence posts, pickle barrels, and teak homes from Indonesia.
There's also a good article on building a home while not on site. Get the builder to take digital photos, among other things. Good communication is even more important...
In The Green Scene, Kenya McCullum points out how important siting your house in relation to the sun is. (Our house is perfectly sited, btw, with the front and back porches protecting us from the rising and setting sun.) Also, use sustainable materials and keep the waste down, and think about your landscaping--placement and plant choices. Think about maintenance and energy saving appliances too.
Another article looks at green paints and stains. Choose a product with low VOC (volatile organic compounds).