If you are booking a hotel on your own, one of the most important questions you can ask is how the hotel or lodge disposes of its waste and sewage. It might not be the most pleasant thing to ask, but if hotels start to realize that guests care about these things, they will be more responsible. This is what makes true ecotourism different from adventure travel. It also gives feedback to the companies it inspects. The most important aspect of an ecotrip is the local guide.
Good companies train local guides, who then become ambassadors in their own communities.
Guides should have a very good understanding of the ecosystem and know what will and won't harm it. The best companies have guidelines for how their visitors should interact with virtually every species they might encounter. Birdwatching is a special concern these days, as so many birders forget that it is more important to protect the species than it is to get the bird on their lists. The general principle is not to disturb the animals in their natural habitat. The place you see the most difficult problem is in East Africa, where there is a very entrenched system of going after the Big Five mammals.