Caravanistan
In terms of practical information on independent travel in Central Asia, Caravanistan has basically replaced the guidebooks. Their regularly updated website provides info on visas regulations, border crossings, itineraries, transportation, accommodation, and general travel advice.
Trekking Guidebook
“Trekking in Tajikistan: The Northern Ranges, Pamirs and Afghanistan's Wakhan Corridor” by Jan Bakker and Christine Oriol is a guidebook that contains 21 treks exploring 5 different mountain areas of Tajikistan. It includes advice on trekking, backpacking equipment, permits and visas, and transport, plus GPS tracks.
Archa Foundation
Based in Dushanbe, this organization (link) promotes mountain travel in Tajikistan and provides services such as camping equipment, trekking gear rentals, GPS tracks and transportation services through Fann Adventure Travel.
Zarafshan Tourism Development Association
This Khujand- and Panjakent-based NGO develops tourism infrastructure in the Zafarshan (Zeravshan) Valley and promotes community based tourism. They support guesthouses, offer tours, and have camping equipment for rent. Link.