Do you mean a small picturesque town, or a small picturesque city? Villages can be very limited, but maybe that's what you want.
I hesitate to say it because I'm selfish and don't want it to get too popular, but Italy's best city in my opinion is Lucca. I've been there 5 times and am always happy to be back. You can spend one day riding bikes on the city wall and eating your way through the old centre of town, and other days on trips. Pisa is 30 min away, the beach at Viareggio & Forte dei Marmi is about an hour, Volterra is close, the Garfagnana is gorgeous and it's just north of Lucca. And if you missed something in Florence, you're an hour away. I'd consider staying in Volterra too.
I've been to San Gimignano and it's amazing, but not a lot to do and lots of tourists during the day. I had a friend who stayed there on gift pass in some Sheraton property and she said it was a magical place after the hoards leave (I'm sure the free luxury accommodation helped a little). If you can stay the night in a place that has a lot of day visitors, it becomes a completely different place.
Siena is also a nice place to park yourself for a bit, although I'm not sure what the day trips are (we moved on to Umbria the time we were there).
I did note back in 2000 when we drove through Colle Val d'Elsa that it looked like a village worth revisiting. Haven't made it back yet.
If you're open to branching out of Tuscany, when we were on the flight coming home from Tuscany years ago, the arty hip guy sitting next to us said "Tuscany is so yesterday. Umbria is where it's at." So the next trip we went to Perugia and I have to say it was lovely!
I hope that gives you something to start with. I don't know anything about SE Tuscany where a lot of the popular places are.