A huge benefit to building a new home is you get to make everything custom to your tastes. If greening your home is important to you, you should consider this as you pick your design features as well. You don't have to compromise your tastes to be green. Beautiful flooring and countertop options can be chosen with Mother Nature in mind. Bamboo is a rapidly renewable resource, so it would be a very green choice for your floors. If you're not crazy about the color and look of bamboo, take a look at woven bamboo. Not only is it often stained in interesting colors and looks more like a grained wood, it's also much harder and more durable than traditional bamboo. And for a flooring option, it's quite affordable.
For countertops, you could go with recycled glass surface like Vetrazzo instead of granite or another stone that is not renewable. The flecks of recycled glass in a product like Vetrazzo come in a variety of colors and will really add a statement to your kitchen [source: Vetrazzo]. It's a little pricey, but the cost should continue to come down as it catches on, as is the case with most green building options. Several large home improvement stores now carry the product, too. Compared to granite, it is a much more sustainable option for around the same price point. And it doesn't stop with Vetrazzo. There are many more sustainable and green options available. Ask your contractor or an expert at your local home improvement store for more suggestions.