To travel on the Pamir Highway in Tajikistan one needs a special GBAO permit, I got my Tajik visa today and it came with an extra stamp:
Is this the GBAO permit?
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Yes, that's it. I just checked my passport, where mine is still in from three years ago, and can confirm mine looks like that too. They check it at the entrance to the area, a few hours out of Dushanbe, and then at many, many checkpoints along the way - at least to Khorog, which is as far as I got unfortunately, before needing to turn back.
Enjoy the many tea stops, the crazy rides, cliffs, and spectacular scenery like this:
and keep an eye out for the odd overturned tank(!).
(edit) If you want an online source, the link Gilles provided backs this up.