I'd like to book the big museums in advance. I found one site where the fee to book was more than the admission to the museum. Where is the best place on the internet to book tickets? Are there any other museums other than the Ufizzi that are recommeded to book in advance?

This is the best way to do it...per a previous poster. I used this route and it was simple. You don't pay the fee up front, and you don't have to use the reservation if you arrive and there is no line. They will give you the fee over the phone and it's much cheaper than all the internet booking sites I researched.

"The easiest and cheapest way is to call Florence 011 (U.S. international access code) 39 (Italy's country code) then 055-294-883 8:30-18:30 M-F and 8:30-12:00 Sat. Florence time. You will get an English speaking operator and in 2-3 minutes YOU CAN RESERVE FOR BOTH. This is through the reservation service at the Uffizi and costs beyond the normal entry fee only about 1.60 euro for the service. This is MUCH cheaper than the commercial booking services."

The other booking that is often recommended is the Academia in Florence (to see David), though a couple of weeks ago, we walked straight in without a booking.

Sue is right. You can use the same number for both the Accademia and the Uffizi, which are the two biggies to book ahead for in Florence. We were awfully glad to have our Accademia reservations in July because we walked right in ahead of the line of 100+.

If you are visiting Venice, people also reserve the Doge's Palace Secret Itinerary Tour in advance. I can find the number if you need that one, as well.

A very useful thread on this sort of information is entitled
Helpful Information on Italy. I don't have the URL, but do a search on it.
It's a compilation of FAQs on many areas in Italy.