There is also the Scavi tour under the Vatican. You can book this through the Vatican's office, but each tour is only 12 persons, so it books up very fast and far into the future. I tried to book in October 2012 for late November 2012 and they were already full. People on TripAdvisor think it's a great tour. Here's the website:

http://www.vatican.va/roman_curia/in...090216_en.html

I sent them an email with several dates in mind, and they replied within 24 hours.