This was easily the coolest thing we did while in Italy.
If you're ever in Rome you HAVE to request a reservation on the Vatican's official Excavation tour. It's a tour of the original necropolis and tombs underneath the papal crypts underneath St. Peter's Basilica. It's led by a Vatican archeologist (ours was married to a Swiss Guard member and took her job VERY seriously, it was awesome) and takes you through the "streets" between the old tombs several stories beneath the floor of the basilica, finishing with the original burial place of St. Peter himself.
Then you go up a level, to the same floor as the Papal Crypts, but in a heavily restricted and guarded area accessible only to high level members of the church and this tour. You go to the Pope's private chapel which is built around St. Peter's tomb and you can see the bone fragments inside from where they opened it to confirm it's him.
Incredible experience that's limited to only 250 visitors per day. A bunch of tour groups claim to offer this, but they just bring you to the Papal Crypts, not the necropolis below or the chapel build around St. Peter's actual tomb.
Check it out:
http://www.scavi.va/content/scavi/en/ufficio-scavi.html