I am in need of some suggestions for some small, quaint Roman towns to visit when I leave Rome, on my way to Siena. I understand Assisi is quite touristy and we don't want that. How about Perugia? Please advise, leaving on Monday!

As I answered in the "Assisi" thread, don't let one person's (including mine) opinion set your schedule.
Assisi is no more "touristy" than most popular hill towns. Believe me, Siena gets very "touristy" as well.This is especially true of any town on the train line and those that tour buses hit.
That said,enjoy the fact that there's a reason why many want to visit these popular towns.
Specifically to your question, what route are you taking? Will you have an auto? How long will you have to visit?

I'll respectfully disagree with jabez if I may. We visited Assisi, Perugia, and many large and small towns in Tuscany, and my experience was that Assisi had by far the highest percentage of tourists (compared to people who live/work in town), and the highest ratio of gaudy souvenir-type shops to nicer shops. I wouldn't descibe Perugia as small or quaint, but it is a lovely city, well worth a visit for its shops, character, and views.

What are Roman towns? That area was settled by the Etruscans long before Rome existed. And, both Assisi and Perugia are not in Tuscany. You need to buy a good book and do some reading.
Are you driving? How much time do you have? For starters, stop at Orvieto and Montepulciano.

I also recommend Orvieto.