Galleria Borghese is a fairly small museum (compared to the Vatican, at least) located in Villa Borghese, but it just so happens to be my favorite. The museum is a little out of the way, on the eastern end of the park and not terribly close to the historic center of Rome, but if you have the time, it’s well worth the trip (plus you get to take a stroll through the park, which is also beautiful). The building itself was the home of Cardinal Scipione, and the collection was his as well. Scipione clearly had good taste, and many of the works are Baroque masterpieces.
Here you can find Canova's nude sculpture of Pauline Bonaparte (yep, that's Napoleon's sister), as well as several excellent Caravaggio paintings (there‘s a particularly striking piece of David holding the head of Goliath). The real highlights, however, are the Bernini sculptures. In addition to a sculpture of David, one rumored to be an early forgery done by Bernini, and one of Scipione himself, three mythological sculptures - Apollo and Daphne, Aeneas Fleeing Troy, and The Rape of Proserpina - are pieces that Bernini finished in his early 20s. The sculptures are displayed so that admirers can get close to them and walk all the way around them, allowing vantage points to take in Bernini's attention to detail. The Rape of Proserpina ("rape" being used in the classical sense, meaning "abduction") is my particular favorite. Pluto's hand squeezes down on her thigh, making her skin puff up in between his fingers, a few tears stream down her face, her hand pulls back the skin around his eyes as she struggles to get away - all perfectly realistic, and all done in marble.
I've heard that you are supposed to call ahead to reserve tickets for the museum, but I went three times and never booked my tickets ahead of time, so I'm not sure how necessary reservations actually are. If you're going over the summer and have a limited schedule, it probably wouldn't be a bad idea. Your ticket will admit you for just two hours, with a half hour visit to the painting gallery included in that chunk of time. The gallery has some interesting pieces by Titian, Raphael, and Antonello di Messina, which can be worth a viewing. But if you're a big fan of Bernini or Caravaggio (his works are displayed in the main gallery), you might want to consider spending your two hours on them - it's just barely long enough.