Similar to Kyrgyzstan, in Tajikistan ecotourism is a wildly abused term that gets slapped onto everything and everyone. For a review of places to stay (eco and otherwise), see accommodation in Tajikistan.
Like with homestays, when it comes to activities, I do not see a difference between independent tour operators and the ecotourism associations supported by foreign aid organisations. They do the same things for the same price and it ends up benefiting the same amount of people in equal ways.
There is no difference, except, of course: ecotourism associations cost money to the donor organisation, in the form of foreign consultant fees. That is why we prefer to work with local independent operators: it is less wasteful, the service is better and, hilariously, it is much more sustainable on all levels.
Responsible travel shopping
Dushanbe: The Bactria centre (location in flux) has a good range of handicrafts for sale from cooperatives and NGO’s.
Khorog: De Pamiri, located at 77 Lenina, offers handicrafts from Pamir craftspeople, whereby most money stays with the makers. This includes feltwork, socks, skullcaps and musical instruments.
Murghab: Yak House, in META’s information centre, offers crafts from locals.