I highly recommend the Best Pantheon hotel/B&B in Rome. I realize it's a terrible name, but the accommodations are fantastic. My wife and I stay here every year when we go back to Italy.
It only has 6 rooms, but it's a great place to stay. The rooms are extremely clean and the hotel is as well. They bring a menu to your room each night to fill out what you want for breakfast. If you want everything on the menu, they'll bring it--it's included in the price.
Find the link included below. We've never stayed at their hotel near the Vatican because we like this one so much.
http://www.bestbb.it/p_eng_camere.htm