500 Year Diary

The Five Hundred Year Diary was a journal kept by the Doctor. Further updates included the Nine Hundred Year Diary, (TV: Doctor Who) the Twelve Hundred Year Diary, (TV: The History of the Doctor) and the Two Thousand Year Diary. (TV: The Girl Who Died)

History
The First Doctor began writing the diary whilst still on Gallifrey, but left it there when escaping with Susan. It was returned to him by his mentor K'anpo Rimpoche, shortly before his first regeneration. (PROSE: The Three Paths)

Following this regeneration, the Second Doctor got his diary out of his storage chest and began to read it, even while walking through the mercury swamps of Vulcan. (TV: The Power of the Daleks)

The Doctor later checked his diary while on Telos to read up on a previous encounter with Cybermats. (TV: The Tomb of the Cybermen)

While on Earth, the Fourth Doctor checked his pockets for his diary, which contained notes he had made about the Sontarans. (TV: The Sontaran Experiment)

While on a planet made of confectionary, the Fourth Doctor checked the calendar in his diary and learned that it was K9's birthday. (PROSE: The Not-So-Sinister Sponge)

The Doctor would sometimes use his diary to check his history. The Fourth Doctor once used it as evidence to prove that he was never the phoney Second Doctor. (AUDIO: Survivors in Space)

By the final time of his fifth incarnation, the Doctor confessed to Peri Brown he tried keeping a diary, not chronological, but "the trouble with time travel is one never seems to find the time". (TV: The Caves of Androzani)
 * It is disputable if he was referring to the Five Hundred Year Diary.

He was still using the diary when Mel was his companion, referring to a note in it. (PROSE: Uranus)

Before leaving the TARDIS, Ace took his Five Hundred Year Diary. (PROSE: The Death of Art) After this, it is unclear whether or not she gave it back to him or the Doctor had a spare.

By the time he was traveling with Lucie Miller, the Eighth Doctor had the Five Hundred Year Diary in the TARDIS library. He used the book to pinpoint which species of alien was threatening Little Morton. He was able to correctly guess that he was dealing with a Quitoxin. (AUDIO: The Young Lions)

Further diaries
The Fourth Doctor provided two volumes of his time logs to search for references to Traken. He hinted he was too busy to still keep track of his travels. (TV: The Keeper of Traken)

The Seventh Doctor owned a Nine Hundred Year Diary shortly before his regeneration into the Eighth Doctor. (TV: Doctor Who)

The Tenth Doctor had a psychic diary written on psychic paper. He explained to Christina that it held everything he saw and felt. The Doctor kept this diary on a desk in the TARDIS's library, but due to a cloud layer in the library's upper stacks, the desk was rained on no matter where it was placed. The Doctor was forced to use a saucepan to catch the rain so it didn't moulder the psychic paper and produce psychic mould and psychic mushrooms. (PROSE: Keeping up with the Joneses)

The Eleventh Doctor kept a journal of the encounters he had with River Song. (TV: The Impossible Astronaut et. al.)

The Eleventh Doctor had a Twelve Hundred Year Diary, which he and Clara read it when the Doctor forgot everything about himself. His memories were returned after reading the book. (TV: The History of the Doctor)

The Twelfth Doctor owned a Two Thousand Year Diary which he used to remind himself of the Mire. (TV: The Girl Who Died)

Other references
While pretending to be an incarnation of the Doctor, Mr Song disguised River Song's diary as a Five Hundred Year Diary. (AUDIO: Signs)

Behind the scenes
The reference book The Doctor's Lives and Times states that Susan bought the Five Hundred Year Diary during her visit on Tiaanamat as a present for her grandfather.