There are many museums in Florence beyond the Uffizi and Accademia Galleries. Museums in Florence are can be divided into 3 types: those run by the Italian national government, which are called State museums, those run by the city which fall under the Florentine Civic Museums office (see the list of those here) or private (such as the Palazzo Strozzi, the Horne museum, the Stibbert Museum).
In order to help you sort out which are which, I've created a list below. This is particularly important when special openings occur, where free entry is offered into State museums only or only to Civic museums, and that's why you need to know which are which.
For example, since July 2014, ALL OF THE STATE MUSEUMS below offer FREE entrance to everyone on the FIRST SUNDAY of every month!!
State Museums in Florence
Uffizi Gallery (now called the Uffizi Galleries, which also includes the Pitti Palace and Boboli Gardens)
Accademia Gallery (+ Cherubini Conservatory Musical Instruments Collection)
Bargello National Museum
The Medici Chapels
Museum of San Marco
The Pitti Palace
- The Palatine Gallery & Royal Apartments
- The Gallery of Modern Art
- The Costume Gallery
- The "Museo degli Argenti": The Medici Treasury also known as the Silver Museum
- The Porcelain Museum
- The Boboli Gardens
Museum of Palazzo Davanzati
Museum of Casa Martelli
Church and Museum of Orsanmichele - free entrance
Hall of Perugino - free entrance
Garden of the Medici Villa of Castello
Corsini Villa of Castello
Medici Villa of Petraia
Medici Villa of Poggio a Caiano and Museum of still life
Medici Villa of Cerreto Guidi and the Historical Hunting and Territorial Museum
The Last Suppers and Cloisters
'Cenacolo' of Ognissanti - Last Supper of Ognissanti
'Cenacolo' of Andrea del Sarto - Last Supper of San Salvi
'Cenacolo' of Fuligno
'Cenacolo' of Sant'Apollonia - Last Supper of Sant'Apollonia
Cloister of the Scalzo
The Carriage Museum (Pitti Palace)
The Contini Bonacossi Collection (Uffizi Gallery) - there are special guided visits planned occasionally, you can see when if you follow the news section here.
The Vasari Corridor (Uffizi Gallery) - this is open to groups organized by tour agencies, see those tours here. The Corridor will definitively close for restoration at the end of November 2016.