We spent a week in Italy last month and I would recommend the following:
Spello: We stayed at the Hotel and Restaurant Basigilia which has a one star Michelin restaurant, nice hotel and parking. Our meal was the most innovative of the trip with fried, stuffed artichokes, lamb and its parts, grilled octopus and excellent wine. We also ate at Il Molino and my mixed grill plate was the best bargin of the trip.
Perugia: Lunch at Antica Trattoria San Lorenzo was warm, friendly with creative dishes made from local ingrediants.
Assisi: In the main square, get in line for the take-out pizza with its thin crust and excellent cheeses and meats.
Siene: Osteria le Loggia, good lamb with the best santo/biscotti plate of the trip.We were, however, ushered up to the second floor with the tourist. Make sure you make a reservation and ask for a downstairs table. Nello la Taverna has a wonderful owner who will make suggestions for your meal. We had beef steak and moist apple cake with santo. In addition, lunch at Hosteria Il Carroccio, Via Casato di Sotto 32 where the pork stew on polenta and veal stew and white beans where excellent. The place was packed with locals and Italian tourist and had a wonderful buzz as well as a generous host (grappa was put on our table and we were encouraged to keep trying...good for our stomachs the host said.)
Marine di Pisa: We overnighted in this town before catching our flight out of Pisa in the morning and, on the hotel's recommendation, ate at Da Gino. Excellent. The spaghetti vongole was not over burden with garlic and the fresh taste of the clams dominated. My husband had a five plate appetizer of fish dishes that could have been a meal. We both ate the catch of the day and shared lemon sorbet drink for dessert.