I've been all over Italy and, to my surprise, the best pizza I found was in one of the most touristy spots in the country: Le Arcate in Anacapri on the isle of Capri. It definitely beat out the famous Neapolitan pizza by a good margin.
The second best I've had is a place like what kumazan described in Rome, but my spot was just north of Termini, the main train station. They had a pizza caprese (raw tomatoes, slightly melted mozzarella and fresh basil) that was to die for. It's all about the quality of the dough.