Silphium was a plant that was used as a contraceptive by Romans and had other medical and culinary uses. They apparently drove the plant to extinction and it no longer exists. This isn't a top level answer by any means, but it was the first thing that came to mind.
You might find this to be an interesting read, as this book is pretty much about your question. Collapse: How Societies Choose to Fail or Succeed by Jared Diamond. Did you know, for instance, Iceland, Haiti, and Easter Island all used to have forests? It's a fascinating read about how societies have collapsed due to environmental devastation caused by mismanagement of renewable resources.