Probably the best-known Buddhist monastic archeological site in what is now Tajikistan is at Ajina Tepa, which has been diligently excavated and published by Litvinsky and others. It’s a fascinating site.
Lesser known, and less impressive in size and sophistication if not in location than Ajina Tepa, is the stupa at Vrang, on the Afghan border in the Pamirs. (It’s at 37° 0′ N 72° 22′ E.)
The stupa seems to be in very good condition and there are supposedly
caves that served as cells for monks surrounding it. There’s also a
Buddha fooprint still extant.
15 Feb 2010 update: another photograph of the same site