In Rome, if you have time, try to see the Borghese Gallery. You need to make a reservation and buy tickets in advance, over the Web, because it's a small, intimate building. The collection includes many superb Renaissance paintings and sculptures. Highlights include Caravaggio's Boy with a Basket of Fruit, and especially Bernini's sculpture Apollo and Daphne, which is absolutely breathtaking.
In Florence, a somewhat lesser known but superb gallery is the Bargello. Again, a smaller museum but one with an outstanding collection, focusing on sculptures. The collection includes Donatello's bronze David, one of the seminal works of the early Renaissance, and my gosh, you can walk right up to it and probably be alone with it.