Who do you think rules Fairmarket and Stoney Sept? We see many towns in Westeros, and all are ruled by a family (Dustins of Barrowton, Mootons of Maidenpool, Rykkers of Duskendale, Footlys of Tumbleton, Whiteheads of the Weeping Town, pretty sure the Ladybrights rule Planky Town, since Alyse is treasurer at Sunspear)

Good question!

The last known ruler of Fairmarket was Halleck Hoare, so it may be that it became a royal possession similar to Harrenhal. 

In ASOS, we learn that Stoney Sept was ruled by a landed knight, Ser Wilbert, who was killed by the lions (probably when Tywin was storming across the southern Riverlands en route to Harrenhal), and that his sons went off to fight for Robb Stark and saw service in the Westerlands, which probably means they died at the Red Wedding.