According to I Ristoranti d'Italia guide (edited by L'Espresso), the following are the best restaurants in Italy, as they have been continuosly at the top of their ratings for the past thirty years. I've divvied them up in terms of geography for convenience. Excepting the famous Enoteca Pinchiorri, none is located smack dab in the middle of a major tourist destination. None are in Southern Italy.
Based near Milan:
Gualtiero Marchesi (Erbasco, Brescia)
Antica Osteria del Ponte (Cassinetta di Lugagnano, Milano)
Antica Osteria del Teatro (Piacenza)
Da Vittorio (Brusaporto, Bergamo)
Based near Bologna:
La Frasca (Castrocaro Terme, Forli')
San Domenico (Imola, Bologna)
In Florence:
Enoteca Pinchiorri, (Firenze), in photo