The one that everybody knows is San Gimignano, a village that, thanks mainly to its famous towers, receives far more day-trippers in summer than it can comfortably handle – at peak times the police impose a one-way pedestrian system in the narrow lanes. That said, the fresco-lined Collegiata is definitely worth coming to see, and San Gimignano also has one of Tuscany's best civic museums.
The popularity of Cortona has similarly become something of an issue in recent years. This perfect hill-town, located within sight of Lago Trasimeno – was relatively unknown prior to the publication of Frances Mayes' Under the Tuscan Sun and Bella Tuscany; nowadays the place entices coachloads of her readers to the place where Mayes realized the expatriate dream of the Tuscan good life.
If it's quiet that you want, why not try instead lofty Volterra, west of San Gimignano? Brooding on a windswept plateau enclosed by volcanic hills, it was described by D H Lawrence as "a sort of inland island," and has an air of being somewhat cut off from the rest of the region. Like Cortona, it was a major Etruscan settlement, and the town's museum are stuffed with relics of that enigmatic civilisation.