I've now been to San Gimignano twice. The first visit, I popped in for a few hours and walked around, thinking that was enough. The second visit, I stayed for two nights and saw a whole new side of the town. For those who have time, this is what I would recommend! In the mornings before the tour groups arrive, the streets are deserted and you can explore with nobody but the local cafe owner in sight. In the evenings, the colours of the sunset are incredible.
 
There's also no shortage of things to do in San Gimignano. Obviously the towers are the most prominent feature and I would recommend climbing the Torre Grossa for amazing views and the Torre e Casa Campatelli to see a different style. But make sure to see the artworks in the Palazzo Comunale and the exquisite frescoes of the San Gimignano Cathedral.
 
Also don't miss two other important churches - Church of Sant'Agostino and Church of San Lorenzo in Ponte.
 
There are also various museums and craft shops that you can visit to fill the days, and the famous Gelateria Dondoli really is all it's cracked up to be! I would also recommend taking a stroll along the small country road called the Via Vecchia per Poggibonsi to get great views of the town and its towers at sunrise or sunset.
 
During the day, San Gimignano feels very touristy but its still authentic underneath with lots of local residents living in the historic centre. Just try to avoid the groups and I think you'll love it.