The Bible was the central book of several religions on Earth.
In 64, the First Doctor criticised Amos, Rayhab and Reuben's Greek translation of Mark, noting it to be "as dry as stale bread". He advised them to follow their inspiration, rather than aim for accuracy. (PROSE: Byzantium!) In 1605, he observed the translation of the Bible into the English language. (PROSE: The Plotters)
In 325, the Fifth Doctor, Erimem and Peri were present at the Council of Nicaea. This conference, which pulled together the major scholars and leaders of 4th century Christianity, defined the biblical canon, in ways that remained largely unchanged for the centuries which followed. It also led to a major philosophical divide between the Doctor and Erimem. (AUDIO: The Council of Nicaea)
A copy of the Bible published in the late 18th century was among the possessions of Bathsheba's family, their ancestors having brought it with them when they were taken by Goibhnie to Tír na n-Óg. The Seventh Doctor thought he may have helped write it. This Bible was later used in David Gibson's exorcism. (PROSE: Cat's Cradle: Witch Mark)
H. G. Wells, during a stay in Scotland in 1885, attempted to hold up a Bible, along with a crucifix, in an attempt to repel a newly arrived Sixth Doctor whom he'd mistaken to be a spirit. (TV: Timelash)
In 2008, Sarah Jane Smith quoted the Book of Revelation in the Bible to Mrs Wormwood. (TV: Invasion of the Bane) That same year, Ianto Jones quoted biblical verses from the Book of Daniel after the Cardiff Rift was opened. Jack told him stop as his chosen quotes referred to the end of days and were damaging morale. (TV: End of Days)
In the 108th century, when Tegan Jovanka used the phrase "pearls before swine", Sven Tornqvist recognised it from the Codex of Lazarus. She said it was from the Bible, but he didn't know what that was. (PROSE: The Crystal Bucephalus)
Behind the scenes
As far as the Doctor's travels are concerned, the televised stories have generally avoided making references to the Time Lord being present at, or involved in, any of the events featured or referenced in the Bible. A notable exception occurs in Voyage of the Damned in which the Tenth Doctor claims that he took the last room at the inn in Bethlehem, which forced Joseph and Mary to find alternative accommodation. The Doctor's purpose for being there is left unstated.
Another possible exception occurs in Planet of the Dead, in which the Tenth Doctor claims he was present at "the original" Easter, though he is interrupted after saying "What really happened..." before he can specify whether he means the resurrection of Jesus (the event Easter commemorates) or the first formal celebration of Easter, and before he can elaborate further as "what really happened".
Books and audios have been far less reluctant to use the early Christian Church as a backdrop for stories.