Updated on September 12, 2012: The Department of Tourism in Florence has a new bus and road map out to help people get in and out of Florence and the surrounding areas. Of course you have to get one at the tourist office, which sort of makes it a Catch-22 situation. Anyway - it has a ton of good info on it, like this little map below showing the locations of the bus stations near the train station:
The map below is now out of date (corrections are in RED) - the Lazzi station is gone (it is now a Burger King), and is combined with the CAP depot. The ATAF Info booth is also gone, and is now located at the southwest corner of the the train station. See the Google map below this one for more details.
And here are some important links for rail and bus transportation into and out of Florence and the surrounding area:
SITA: http://www.fsbusitalia.it (Arezzo, San Gimignano, Siena, Volterra, The Mall)
CAP: http://www.capautolinee.it (Prato, I Gigli)
Lazzi: http://www.lazzi.it (Arezzo, Lucca, Montecatini Terme, Prato, Viareggio)
Autolinee Toscane: http://www.autolineetoscane.it
Here is a map from Google showing roughly the same area: