Todi or Spoleto

Christine, nestled on a hilltop, Todi is quite small an very charming; Spoleto is a small city with many walk able sites. Perhaps your choice will be made on ease of access (bus or train schedules) or time available.
Ciao, Craig

Are you driving up from Rome for the day? If so, it is nearly 2.5hrs each way. I would just concentrate on Assisi as there is so much to see and enjoy there.
If you want to stop somewhere else consider Spello over Spoleto as it is much smaller and it would be easier to fit in a stop than Spoleto.

mph has a good suggestion, Spello is only a few kilometers from Assisi, one train stop. If you have a car, drive to Trevi, also near Assisi.

There are a few Franciscan sights that are a long walk, but you can drive or if you don't have a car just hire a taxi in Assisi - the driver will pick you up, drop you off, meet at an appointed time and repeat for the next sight. A friend and I did this for €25.

I love Todi but public transportation is infrequent.

Spoleto is an agreeable place, but can't really be enjoyed just as a break on a day trip. And if you're on the train, it's something of a half hour walk from the railway station to the city centre.
Foligno - another few kilometres from Spello - is surprisingly interesting and might be a welcome change from all that climbing in hill towns and the tourist crowds which come with it. The railway station is close to the centre.

I loved Spoleto; it's a charming little city with a beautiful Roman arena. I wa there during black truffle season and had an amazing dinner. It's quiet and very close to Assisi. I was only there for one day and it was enough time. There is a shuttle from the train station to the main square, you do not have to walk.