well when you talk about “green building” ita not just about picking a green material, but how to use materials in a way that would for instance make your floor have better insulative properties.
In building there are very few truly green materials, but you can take materials that are not green and do some very energy efficient stuff with them.
So it comes down to a total life cycle cost + how you use the material = green building. I hope that makes sence…
To answer your question, there are many different types of flooring that you can use, from cork and bamboo to natural fiber carpets. You can always go with a natural fiber carpet which is green and will give you better insulative properties which will help lower yor energy cost.
Here is a great little site that looks at each material separately:
http://www.greenfloors.com/