Massive! The amount of antiquities housed in that one area is amazing. I'll start with the basics. The museum is open from 8:45am to 3:45pm. The last persons are allowed in at 2:20pm. When you get to the museum, you'll see the line stretching around the street and probably to the front of the Vatican itself. That is normal, and it should only take about half an hour to get inside. They usually have between 4-6 metal detectors going. We were also surprised to know that we could take our baby's stroller inside. We had to check it in when we went inside St. Peter's. Photography is allowed in the museum in certain sections. You are not allowed to use flash photography near the artwork or tapestries, and no photos at all in the Sistine Chapel.
The major sections the museum has are: Egyptian & Assyrian art, Greek & Roman art, Etruscan & Italic art, early Christian & medieval art, 15th-19th century art, and modern religious art. Have a plan of attack before going because it is really easy to get turned around and end up missing what was on your list.
Just as all roads led to Rome, all halls led to the Sistine Chapel. It is the last section in the museum before the exit. If time permits, see everything you want to before hitting the chapel. We were on a time crunch and wanted to make sure we saw the Sistine Chapel. We were then going to loop back around to see whatever else we could see before time ran out, but were forced to exit. The museum is set up mostly as a one-way journey, so see everything you can before moving on. There are guards all over the place and they will instruct you to keep moving, more so if a particular area is getting too crowded.