Where to stay in Tuscany and traveling by public transportation?

Katherine, in Tuscany, you will find the train going to some places but not many others. So many of Tuscany cities, towns and villages do not have a train stations. San Gimignano, Volterra, Cortona, Montepulciano are examples of towns without train stations. You can get to these towns by bus but these bus systems hub out of Florence, Siena, Chiusi, Poggibonsi, Pisa and a few other cities. In general, they don't go from one small town to another. They first go back to the hub where you pick up a different bus. You will find this quite limiting as you won't be able to see as many places as you thought. If you are planning to travel in Tuscany by bus on Sundays, forget it. The bus schedule are quite limited on Sundays (Festivo).

For 4-5 days in Tuscany, you would be so much better off renting a car. Stay at a local agriturisimo somewhere in Tuscany (this site can recommend many), and drive all throughout Tuscany. Just don't park inside the city or town walls. You will see and enjoy so much more of not only Tuscany but possibly a bit of Umbria as well.

I agree about renting a car--at least if you want to really see many great hill top cities in Tuscany. You can see 3 cities in one day versus one via bus.

Roads are well paved, and the back roads are scenic, if a little crooked. Navigating is no problem with good road signs pointing you to other cities.

Renting a car is the easier way to get around Tuscany - but with careful planning (bus schedules, etc) ahead of time you can definitely do Tuscany without a car if that is your preference. I would advise staying in a city that does have a train station.
(I'm certainly biased but Arezzo could be an option - the train station is very accessible and from there you can take the train to Florence in an hour, Cortona in less than half an hour. To get to Montepulciano you can take the train to Chiusi and the bus from there. Although the bus schedule is a little limited, I thought the bus ride from Chiusi to Montepulciano was beautiful. You can take a bus directly to Siena.) Knowing which Tuscan towns/cities you are interested in seeing will help to be more specific on if it's doable by public transportation or not.

I've visited many towns in Tuscany without a car, usong buses and/or trains). Train stations are often outside the main city (Cortona's, for example, is a few miles from the city but a taxi cost less than €10 two years ago). If you want to visit vineyards or very remote hilltowns, a car is more efficient, but you can hire a driver for an excursion like that.

You could do something like Siena and Orvieto by train. The views of and around both places is spectacular, and if 2-3 days in Siena itself is too much for you, there are always small tours (wine tasting, etc.) you could do outside of the town. I won't spend time working out all possible towns since I have no idea of your interests, but you can play on the train sites (bahn.com for easiest site maneuvering and trenitalia.com) and see where the trains go...then figure out which destinations look good to you!

Not everyone is comfortable driving in a foreign country, and if you're one of those people, my advice will be to stay in Florence. Florence is THE transportation hub for Tuscany, and from Florence you can do many day trips, including Siena, and even take full day wine tours which will allow you to see the countryside without driving. Florence is worthy of at least two full days and nights, just to see everything she has to offer. I've been three times, each time spending an entire week there, and day-tripping to the other towns. I love Florence!

I would suggest staying someplace along the train route between Florence and Lucca, because you can get to the from the Cinque Terre from there. Lucca would be very nice. We stayed in Prato, about a 15 minutes train ride from Florence. Prato is a small city but very old and interesting. We stayed at a great place, Villa Rucellai. The only problem is that the villa is a very long walk from the center of town and the train stations. A lot depends on where your trip starts, since the Cinque Terre are north of Tuscancy in Liguria. The high speed trains go through Florence to Rome so if you start in the Cinque Terre, then travel toward Florence, there a many towns along the train route.

I can recommend Lucca as a wonderful smaller town. For about a week, three of us (one couple and one single) stayed at the Hotel Puccini (hotelpuccini.com), which is right around the corner from a small square with a statue of Puccini and a homey little bar (The Caffette). Hotel Puccini was great, and a good place from which to begin day trips! Attentive owner, yummy breakfast, clean. No A/C, but with Casablanca fans and private bathrooms. The little bar was a good base of operation. Two wanted to do this and one wanted to do that, and we'd meed afterwards at the little bar (outside seating). No problem waiting for someone with a glass of wine or a beer in front of you while you journal or read. Free entertainment often popped up in the little square. My room overlooked the square.

With a car, choose any location between Florence (near Impruneta) all the way down to near Siena, in any town roughly along the freeway (Raccordo Firenze-Siena).
Without a car, stay in Florence proper and day trip to other towns from Florence. Florence is a big city, but in the old historical center it has a smaller town feel since cars aren't allowed.