Flying in and out of Florence for 10 nights in September.. Need help with itinerary.

I think a week in Florence, with side trips, sounds excellent. While you're doing your side trips, you're bound to think of things you want to do once you get back to Florence. The only alternative I can think of is to do 5 nights in Florence, 2 nights in Lucca, then CT.

Nothing wrong with a week in Florence. You might split the week between Florence and another town, perhaps Assisi or Siena, and daytrip from there as well. Or, spend a few days in the Lakes area.

We spent a long weekend in Florence. On Monday, we picked up a rental car and headed 45 minutes south to an agriturismo--outside Certaldo and San Gimignano..

With a rental car, we were free to visit the many hilltowns--many of which are not on train lines. We enjoyed San Gimignano, Certaldo, Volterra and Siena.

Then we headed about 90 minutes south of Siena to the Umbrian hilltown of Orvieto--another great stop. We turned in our rental car across from the train station and hopped on a local train for the 70 minute ride into Rome Termini.

I hear Lucca's very nice, but it sounds a little quiet for me. I do want to visit the C/T next trip, however.

We spent three nights in Florence, which I felt was enough. Getting in and out of Florence in a rental car is a hassle in my opinion.
We picked up rental car and spent four nights in Pienza - great location for exploring surrounding hill towns and easy to navigate in and out on a daily basis. I think any of the larger hill towns would be a good base - we wanted something big enough to have a couple of choices for restaurants in the evening. Drove from Tuscany to CT (dropped car in La Spezia?) and did final three days in Manarola.

Thank you all for your advice. Unfortunately we are unable to drive. Are there any towns we can visit via train or bus?

If you don't plan to drive, basing yourself in Florence to visit other Tuscan towns is probably the best choice. Somebody suggested to split your Florence nights between two bases: Florence and Siena (or Lucca). You could do that of course to get a feel of staying overnight in a smaller city. On the negative side is that checking in and out of hotels is a time wasting hassle especially if you are moving only to a location that is only one hour away from Florence.
Whether you decide to split your stay between Florence and Siena, or not, remember also that for your last night before the flight home you must spend the night in Florence as the flight is likely early morning. Therefore I would leave Florence for last no matter what. In other words, since you will probably arrive at FLR in the early afternoon, I would go straight to the Cinque Terre. I know that would make it a very long travel day but the Cinque Terre would be a perfect environment for getting rid of the jet lag. After the Cinque Terre you would come back to Florence for the rest of you vacation. If you decide to spend a couple of nights elsewhere (Lucca or Siena) do so before Florence. In other words leave Florence for last. If you don't split your Florence stay, you might even spend an extra night at the Cinque Terre and take a day trip to Portofino or Portovenere from there. It's up to you, it depends if you have a preference for city life or small fishing village life.
Florence is Tuscany's capital city and transportation hub, therefore from Florence you can reach any town, no matter how small, with either the train or the bus (some towns are not served by rail). Just remember that bus service is very reduced on Sunday, therefore do not plan day trips by bus on Sunday (trains have more or less the same level of service every day, including Sunday).

For a description of many towns and villages in Tuscany look at this website, a very comprehensive guide to Tuscany:
www.borghiditoscana.net
Many are close enough to be visited as a day trip from Florence. Just check on the map where they are. Some villages are a bit of a distance from Florence (especially those in the Province of Grosseto) and are too far to be visited in a day without a car.