Neat BBC article about "secret" libraries in various locations, including Egypt, Syria and the Vatican.
The Vatican Secret Archives holds treasures including:
"correspondence between the Vatican and figures such as Mozart, Erasmus, Charlemagne, Voltaire and Adolf Hitler, there is King Henry VIII’s request to annul his marriage to Catherine of Aragon... The archives also contain Pope Leo X’s 1521 decree excommunicating Martin Luther, a handwritten transcript of the trial against Galileo for heresy and a letter from Michelangelo complaining he hadn’t been paid for work on the Sistine Chapel."
It's not really secret, but it is private, open to scholars only. And it's protected by the Swiss Guards.
While in Rome, I recommend you visit here instead. It is a dream of a bookstore.
I wonder if Michelangelo ever got paid.