We arrived in Bishkek in June 2008 with the intention of getting our other Central Asian visas right here in Central Asia. We found the Tajikistan Visa was pretty easy to get and I thought I'd provide some information for other travellers since I've seen a lot of speculation on the Internet.
The Tajikistan Embassy is pretty hard to find as it is in the middle of a residential neighborhood. We had a Taxi take us for 100 som. The embassy looks like a big wall with a garage and two doors. The only signage is in Russian and it took us a few seconds to find the cyrillic letters for Tajikistan. There are no posted hours but the Lonely Planet says they are open from 9-11 Monday-Friday. We showed up at 9:45.
We rung what looked like the main doorbell and a few seconds later the door opened and a gentleman looked out. I asked for a "Visa" in English and he nodded, closed the door and vanished. A minute later the door opened again and he handed me a Visa form. Then he closed the door again. I rang the doorbell a second time to get a form for Lara, and then we sat on the lawn and started to fill out the form. About 5 minutes later the door opened again and he gave us a bench to sit on.
Once we had filled out the form we rang the bell again. He opened the door, nodded, and vanished. We waited. And waited. We talked to some Iranians who were applying for a Visa, and then waited some more. Finally a woman came out, looked over the forms, and then told us in English that we would have to write a letter explaining why we wanted to go to Tajikistan and what towns we wanted to visit. She gave us a piece of paper and Lara wrote the letter. Luckily I had taken along a map so I listed a bunch of towns along the Pamir highway.
Once we had written the letter, we rang and waited again. We were then told to go to the other door, where we were finally allowed inside the compound to the Visa office. We handed our forms, passport photos, and a copy of our front passport page to the lady. She gave us back a stamped copy of the passport front page with a note explaining that the Tajikistan Embassy had our passports. A 30 day Visa costs $50 dollars + 50 Som, and a 45 day Visa costs $60.00 + 50 som. There seemed to be no problem getting the 45 day one. We were told that it take 4 working days and we could pick up the Visa at 10:00 AM.
If you are travelling to Tajikistan and found this information useful, please let me know by leaving a comment.