Going from Dushanbe, Tajikistan to Samarkand, Uzbekistan via Panjakent is pretty straightforward. In Dushanbe, the shared taxis to Panjakent leave from a station about 10 km north of the center at Map Location: 38.648057, 68.769269 . Bus 3a goes to or close to that station or a taxi from the center will charge around 30 somoni.
Shared taxis to Panjakent charge around 80 to 100 somoni per person and leave when they are full. The key is to find a taxi that is almost full and go with them. This is difficult since the taxi drivers swarm potential customers and will say anything to get their luggage locked in the car until they have enough people. Don't commit to a taxi unless you can get a confirmed head count and by all means don't let them take your luggage hostage.
The drive to Panjakent takes about four hours with a bathroom and snack break about half way. For people prone to carsickness be prepared with a plastic bag or something else to throw up into. The mountain crossing is all curves and the drivers steer violently.
In Panjakent, shared taxis to the border leave from the bazaar and also charge around 8 to 10 somoni and can be paid either in Tajik or Uzbek somoni. There are money exchange offices around the bazaar. The drive to the border takes about 30 minutes.
Depending on the crowd, the border crossing usually takes from 30 minutes to an hour. The Tajik exit had the biggest crowd of about 15 people. The gate guards check papers before letting people enter the offices. The guards and border officers are very friendly and enjoy practicing their English. For the entrance into Uzbekistan there are immigration/customs forms but apparently are only required for the locals.
After entering Uzbekistan, there is the usual group of aggressive shared taxis, marshrutkas, and big bus 273 which goes to Kaftaxona station where other buses continue on to the center of Samarkand. Depending on the type of transportation selected, the ride to the center of Samarkand takes around 30 minutes to an hour.