The regional trains from Santa Maria Novella reach the main Tuscan cities in under two hours, and that single number sets the shape of a day out in Tuscany. The smaller places are the exception: for San Gimignano and Montepulciano the same page suggests a car.
Pisa: One Square, One Decision
Pisa is the shortest run of the four, and the reason to go is a single square. Piazza dei Miracoli, a UNESCO site since 1987, holds the Leaning Tower and a cathedral with a gilded coffered ceiling. The city was a maritime rival of Venice before it was a university town, and it has been a center of education for centuries, which is why the streets off the square feel lived in rather than staged.
The decision is whether to join the posing crowd in front of the tower or watch it from the edge of the lawn. Both are honest; the latter gets you back on a train sooner.

Siena and San Gimignano: Two Hill Towns in One Day
Siena is the medieval counterweight to Florence, and the two cities read as different centuries. Its cityscape is dominantly medieval, the action collects at Piazza del Campo, and the Gothic cathedral sits above it; UNESCO listed the historic center in 1995. San Gimignano, which joined the UNESCO list in 1990, is the smaller stop, and its towers are what people photograph.
Pairing them is the standard solution, and it is sold in two shapes: an 11-hour day from $89 that covers Siena and San Gimignano, and a longer loop from $118 that adds Chianti and Pisa. The difference is not quality but stamina, since the longer version spends more of the day in a seat.
One geographic note from the same page: Siena sits with Chianti to its northeast, San Gimignano to the west and Montalcino to the south, which is why it works as a base for wine as well as a day trip.

Chianti: The Wine Detour
Chianti takes its name from the ground the grapes grow in rather than from a method, and the bottle most visitors recognize is one of several wines the region makes. The Tuscany page lists Brunello di Montalcino, Vino Nobile di Montepulciano, Morellino di Scansano and Vernaccia di San Gimignano beside it, which is the practical hint: one tasting will not cover the range.
No pass is needed to visit wineries. Booking ahead is advised at the well-known estates in Chianti, Montalcino and Bolgheri, and a five-hour Chianti wine tour runs from Pisa for travelers whose trip splits across cities.

Val d'Orcia and Montalcino: The Long Southern Day
The southern run asks the most of you. Val d'Orcia has been a UNESCO site since 2004 and Pienza's center since 1996, Montalcino is where Brunello comes from, and a stop at Sant'Antimo Abbey lets you hear chanting inside the walls.
Montepulciano is one of the places where a car beats the train, so this is the day to join an organized trip or accept a slower rail route rather than improvise.