Whether you like it or not, you'll probably end up spending at least one night in Murghab. Despite rumors of possible guesthouses or hotels, the only actual option that I've encountered was to stay at one of the local home stays. Some of them are more 'official' and some of them less. Ask around to find one. I can recommend the place located here: http://goo.gl/maps/P4Uqt
They will provide you basic accommodation and some food - nothing fancy of course - but they are really nice people over there. Don't get your hopes too high on electricity and if you're looking for a hot shower - keep in mind that they actually need to boil the water on a wooden-run stove, so if you can afford to smell a little bit funky for a little while, take it into consideration.
The Chinese truck that gave me my ride to town was slowly pulling into town, long after the sun had already set. Me and my travelling partners were tired and hungry, and so we set about to find a bed to rest ourselves. We headed out for the most obvious option for backpackers in Khorog - the Pamir Lodge. If Tajikistan has anything that might be defined as a 'backpackers mecca' - this would be it. This guesthouse gathers most of the budget travelers in Khorog - trekkers & cyclists altogether. It offers some invaluable opportunity to socialize with some other people. The place itself is OK at most, so don't expect to feel like you're at home - but it is mostly quiet and there is a nice yard where you can hang out. The toilet over there looks like you worst nightmare most of the time, and this is probably due to the fact that at least 30% of all guests there were experiencing some sort of 'gastrointestinal issues' (endemic to almost all travelers in Tajikistan). Sharing stories and laughs with fellow travelers is one thing, but sharing a toilet with them... That's a different story.
If you're willing to part from a little extra cash (about 15$), you can indulge yourself and head out for any of the handful home stays around town. In order to find them, get directions and information from the local PECTA (Pamir Eco Tourism Association), on which I will elaborate in the following tip. I can highly recommend the home stay located just across from the Pamir Lodge and next to the local school (here: http://goo.gl/maps/8mxl0). Lalmo, the lovely owner and her family seem to very experienced with hosting travelers and they will take very good care of you - as evident by the notes past visitors hadleft in their guestbook. For extra payment you will be treated with dinner & breakfast as well. Lalmo has already gained herself quite a reputation, so you might find her house literally full with backpackers when you arrive, but if you arrive at September or October, you'll likely to be alone in a room to yourself.