I like taxi and walking. Make certain it is a metered cab.
When I visited the Vatican museum & Sistine chapel, the hours were 8:45am to 1:45pm. If still so, plan accordingly.
Beware the pickpockets. Pin your valuables to your underware, and use a hotel safe. They take everything they can grab, not just valuables. Great way to loose your extra pair of glasses.
If you are only there a week, forget side trips that take more than an hour or so of travel. FLR is over two hours travel time each way. From the time you start toward the train to the time you get back, you will spent upwards of 8-10 hrs in travel and wait time.
[This message has been edited by slawecki (edited 04-17-2002).]