This museum is amazing...so many paintings, sculptures, tapestries, maps, etc. One could stay here all day and still not see everything! Every detail is amazing. I spent over half of my time here looking up at the ceilings...endless beauty!
One very important suggestion about visiting the museum: don't go there first thing in the morning unless you have a tour to meet or you don't mind standing in line for 2 hours! We went around 12:30 p.m. on a Wednesday and practically walked right in! The Sistine Chapel is amazing as well. They are very strict about pictures and talking in there, so remember to be respectful!

We booked a four hour tour which consisted of a visit to the Vatican museum, the Sistine Chapel and St Peter's Basilica. We booked this with http://www.rome-museum.com/tickets.htm and I would definitely recommend it as the tour guide really knew his stuff and made the tour very interesting.
As we were part of a tour group we were able to miss the queues which was brilliant.

The Museum, Chapel and Basilica receive on average 20,000 visitors a day so as you can imagine there wasnt really much space anywhere.

The museum was the longest part of the tour and there were so many facts about Rome etc that you would never know unless you had a tour guide.

The Sistine Chapel was a bit of a let down as it was filled to the rafters with people. You were asked to stay silent and not to take photos when in the Chapel however both these requests were ignored which made the experience less enjoyable. However the sight of the paintings on the wall and ceiling were absolutely breath taking.

St Peter's Basilica was definitely my favourite part of the tour. It was so spacious and it is the largest chruch in the world. We were informed that it is so big that you could fit the Statue of Liberty into it.

I don't know how this isn't in first place among the must see places to see in Rome. The site is an awesome walk through time. While I don't consider myself religious, it is amongst the most revered historical sites in the world, this is second to none.

I have been to the Vatican twice; once in Nov and once in late Dec. There is absolutely no need to book a tour just to avoid long lines. We arrived outside the museum at 9:00 to meet our group by 9:15. There was a very small line for the regular folks who didn't book ahead. We watched one family and they were in the door within 15 minutes. We waited for our group and finally went to the entrance at 9:30. Then, due to the disorganization of all the tours, we waited another 30 minutes just to get inside!!! After entering the building we waited again for 10 for our guide to buy our tickets. DO NOT BOOK WITH ROME MUSEUMS TOURS. They are disorganized and give horrible service. When we came out of the museum at 12:00, the lines were nonexistant. If you go in the winter, don't worry about waiting too long!