A real wood floor
Natural materials have been used for thousands of years. When the structure finally decays—sometimes only after hundreds of year—no polluting substances remain. They just return to the earth, unlike materials used in construction today.
When our house was built in 1938, they used real wood floors throughout and real cedar siding. Of course they used natural materials back then, what else would there have been?
Fortunately, we used water-based polyurethane to seal the floors, but we made some mistakes.
Our vinyl siding
Unfortunately, we covered the cedar clapboards with vinyl siding. It was a convenient choice at the time, but we later discovered that vinyl is not a good product to use because manufacturing and disposing of it is hazardous to health and to the environment. Besides, it now seems a shame to have covered up beautiful wooden clapboards.
Why did we do it? Economics played a big role. The south side of the house was constantly peeling (maybe it hadn't been maintained properly sometime in the past?), and it was extremely expensive to repaint every eight years, given the size and height of the house. Unfortunately it was much, much cheaper to cover it all up, and it looked better than peeling paint.
Getting a new roof
Another big item is the asphalt roof material. We bought quality roofing materials so I hope it lasts for another few decades rather than having to be replaced again, but when it does go bad, that's a lot of material to send to the dump. I hope by that time there will be better alternatives available.
All of these problems are proportionally larger as house size increases. Even if we had used these same materials, the impact of their use in our much smaller old Cape Cod would have been much less (though just reducing bad stuff isn't a solution, either.)
Unfortunately, in the kitchen we chose vinyl flooring and formica countertops, and in the bathroom, we used Corian (a synthetic product) and fiberglass.