Elizabeth II

Elizabeth II became the Queen of Great Britain in 1952 at least until the late 2000s.

20th century
The alien Wire attempted to take the energy from the millions of Humans watching her 1953 Coronation on their televisions. However, the Doctor foiled the Wire's plans. (DW: The Idiot's Lantern)

Students at Brendon Public School (as well as the rest of Great Britain), where the Brigadier taught, celebrated the silver anniversary of Elizabeth II's Coronation in 1977. (DW: Mawdryn Undead)

In 1988, her path almost crossed that of the Doctor (who almost but not quite recognized her) at Windsor Castle as she walked her pet corgis about the grounds. (DW: Silver Nemesis)

Elizabeth II was also apparently no longer on the throne at the time the Doctor reunited with The Brigadier for an adventure "several years" into Ace's future and therefore probably sometime in the 1990s. (DW: Battlefield)

Queen Elizabeth was briefly deposed by the Ice Lord Xznaal in May 1997, but was later restored to the throne and her Re-Coronation was held on 23rd November. (NA: The Dying Days)

2000s
In 2001, Dr. Who, a fictional duplicate of the Doctor, tried several times to assassinate her, convinced she was the leader of an oppressive regime. During an appearance in Sheffield he eventually succeeded, but the self-doubts of his accomplice Jason, coupled with his own essentially fictional nature, meant that the Queen survived after all. (NA: Head Games)

On Christmas Day 2006, the blood control powers of the Sycorax (operating out of a ship hovering over London) threatened to make Elizabeth II, as well as the rest of the British royal family jump off a roof and kill herself. (DW: The Christmas Invasion) After the Battle of Canary Wharf (DW: Doomsday) in 2007, the Queen ordered the immediate closure of Torchwood 1 (WEB: torchwood.org.uk). This, as well as the "Christmas Star" incident later in 2007 (DW: The Runaway Bride) which also happened in London, led to the evacuation of citizens when the next Christmas came around in 2008. The Queen, however, staunchly decided to remain in Buckingham Palace.(DW: Voyage of the Damned, referencing DW: The Christmas Invasion and DW: The Runaway Bride).

During the evacuation, the alien Titanic] began to fall out of Earth's orbit, with Buckingham Palace as its impact site. The Doctor contacted the Palace and uttered a pre-arranged code number that resulted in the immediate evacuation of the Queen and her staff. The Queen could be heard thanking the Doctor by name as his piloting skills averted a crash ([[DW: Voyage of the Damned).

In Easter in the late 2000s, the Doctor left the TARDIS in Buckingham Palace gardens, telling Captain Erisa Magambo that the Queen did not mind and that they were friends. (DW: Planet of the Dead)

Other timelines

 * The regime of a fascist parallel England had the British royal family executed. Presumably, this would have included Queen Elizabeth. (DW: Inferno)
 * Elizabeth II was not on the throne another parallel Earth; on that world, Great Britain was a republic governed by a president. (DW: Rise of the Cybermen)
 * In a nightmare alternative timeline created by the Trickster, the starship Titanic did hit Buckingham Palace and caused a nuclear explosion. The Queen's fate in this reality, however, remains unrevealed. (DW: Turn Left)

Minor references and mentions

 * The Doctor theorized that the royal family including Elizabeth II were werewolves after Queen Victoria was attacked by one. (DW: Tooth and Claw)

Elizabeth II and Doctor Who
Elizabeth II reportedly enjoyed viewing classic Doctor Who and, when she met members of the BBC Radiophonic Workshop commented on their connection with the series. The British press has reported that she now watches the new series.

Elizabeth II on Doctor Who
Archival footage of the Queen's coronation appeared in The Idiot's Lantern. Reportedly, Producer John Nathan Turner attempted to get the Queen to appear as herself in Silver Nemesis, but was unsuccessful. An uncredited Mary Reynolds played her instead.

Other information
According to Doctor Who: The Writer's Tale, Russell T Davies originally planned to end Voyage of the Damned with the Titanic actually destroying part of Buckingham Palace (though the Queen escapes). Rather than cheering the Doctor from the ground, Elizabeth (in keeping with her ancestors Victoria and Elizabeth I) would have been heard cursing the Doctor. This ending was scrapped as being too negative and special effects-intensive.