Do any of the museums in Rome require a reservation in order to avoid lines? My guidebook mentions making reservations at the Uffizi and Accademia in Florence, but I didn't see anything about Rome.
I remember something about Borghese needing reservations as they limit the number of people in the museum at a given time. However we showed up around 9:00 to see what was available to reserve later in the day and we were able to enter right away. This was also mid November, and in the middle of the week, so we got lucky.
The Borghese is the only one to my knowledge.
Borghese required, Vatican Museum (Not St. Peters) you can go through a tour agency to avoid or get in a much shorter line for extra Euros.
The Borghese is very well organized and a great galleria. The entrance times are 9, 11, 1 and 3. You arrive about 30 minutes in advance to check in. You can reserve online, but not pay until you get there. You will have to check your bag - they give you a key to a locker. No cameras.
This museum blew me away and was the highlight of my Rome trip in December. The park surrounding it is a great place to walk/picnic.
One thing to note about the Borghese is that they very rigidly enforce a two hour limit on visits there, which is barely enough time to see everything in my opinion.
Golden House of Nero required reservations last time we were there.
There are several passes that get you in several sights and let you go around the que.