Rome Borghese Galleries requires a reservation. If you are going to buy the Roma Pass, you need to call to book. You can also ask your hotel to make a reservation for you - give them the day and time you want. You need to get there about 45 minutes in advance to pick up your tickets, check large bags and rent an audio guide (recommended, not required). If you have the Pass, that gets you into the Colosseum. To avoid the inevitable lines at the Vatican Museums, you should reserve a timed entry in advance or book a tour. If you reserve a timed entry, take the printed reservation with you and find the short security line. Then you go to the reservation desk to pick up your tickets. There is often a long security line to get into St. Peter's. There are 3 ways to avoid it: 1 go early in the morning, [2] go with a tour that includes the museums and the church, or [3] when you get to the Sistine Chapel at the museums, attach yourself to a group that's leaving through the right-hand door. It's a short cut to the church (without a security check because you've already done that to get into the museums) for groups. Sometimes guards let individuals use it, instead of the left-hand door that takes you through a couple more miles of museum back to the entrance. From there it's a good 10 minutes walk to the church on your own, and then you have to line up for the security check. Note that if you have a large back that you had to check at the entrance to the museum, at some point you'll have to go back to the entrance to retrieve it.
Florence There's a museum card you can buy so you don't have to book in advance. Others will have more info on that.
Venice I believe you can book in advance for St. Mark's Basilica. If you want to take the Secret Itineraries Tour at the Doge's Palace, you need to book that in advance - there are few places and it sells out. You can look at the various pass options here. If you don't choose a pass, you may want to buy the Doge's Palace in advance, the lines can be long.
Pisa Book in advance if you want to climb the tower.
I don't think there's anything in your other places that needs to be booked in advance. There are options for passes in Naples/Campagna that may suit your needs, depending on what you plan to see.