Before you go:
Best to obtain an evisa and GBAO permit in advance. This has been available since June 2016, and should be completed only through the official site. This option is for single entry visas only. If you wish a double entry visa, you need to use this system to apply for two different visas.
If you do not wish to or cannot apply for an evisa, then seek an embassy that also provides a Gorno-Badakshan Autonomous Oblast (GBAO) region permit. I obtained mine from the embassy in Almaty, Kazakhstan and the permit was issued for free whereas it will cost approximately $50 if obtained in Tajikistan. However, not all embassies will issue this permit, so check in advance. You need to list all the GBAO regions you wish to visit on the form, so include Darvaz, Ishkashim, Khorog, Murghab, Rushan, and Vanj.
Due to Tajikistan being a very mountainous country, you could often be travelling at altitudes of greater than 4000 metres in the Pamir Mountains (the Pamirs), thus brining warm clothing and/or items that can protect against the wind is essential.
Accommodation: A healthy range of accommodation is on offer in Dushanbe, but it becomes far more limited when leaving the capital. Some places such as Khorog or Murgab do have proper hotels but almost everywhere else will be guesthouses with shared (and mostly good quality) bathrooms. It is also possible to utilise a home stay or yurt stay in the Pamir region, and these can be found when arriving in a town.
Note that where electricity is available in the Pamirs the voltage can be so low that the lights barely illuminate and batteries charge at a painfully slow rate. In Murgab, I found that waiting until very late in the evening when consumption drops sees the lights brighten and the batteries recharge at a normal rate, so consider charging overnight instead of at peak usage times.
Food: Similar to accommodation, Dushanbe possess the widest variety of options, but once you leave the choice of cuisine is restricted to local Tajik or Kyrgyz fare. Even in larger popular centres such as Khorog and Murgab, food options are very limited, so you will be eating only local cuisine during much of your time in the country.
Transport: Transport is limited in Tajikistan once one leaves the confines of Dushanbe. The most common form of transport is a shared taxi – and these are usually a 4WD/SUV. However, they drive long hours and into the evening along some perilous roads. If you can afford to do so, hire your own driver and vehicle which will enable you to stop to admire the stunning scenery, especially along the road that skirts the Afghanistan border.
Once in the Pamirs in the GBAO, even shared taxis are rare and you may wait days for a vehicle. Here it is almost essential to organise your own transport to take you through the region unless you possess a lot of patience (particularly if you wish to travel south from Khorog and east from Ishkashim along the Afghanistan border) and a bit of luck.
Permits: You will need to obtain the GBAO permit if you wish to visit the Pamir Mountains, which is the main reason for coming to Tajikistan. As mentioned earlier, try to obtain this for free prior to coming to the country. If you do wish to travel the areas of Sarez and Zorkul you are likely to need a special permit but these can only be obtained from within Tajikistan. More information on permits can be found from the excellent Carivanistan site.