Miracles were unusual but beneficial phenomena usually attributed to supernatural intervention. In the words of the Eleventh Doctor:
The universe is big. It's vast and complicated and ridiculous, and sometimes, very rarely, impossible things just happen and we call them miracles, and that's the theory.Eleventh Doctor
The evacuation of Dunkirk was seen as a miracle by the people of England. (PROSE: Timewyrm: Exodus)
The Latter-Day Pantheon used their reality-warping abilities to perform many miracles in New York City in 1965, leading to many believing them to be gods. (PROSE: Salvation)
Lolem believed that the disappearance of the Second Doctor and Ramo was the miracle of Amdo having eaten them. (TV: The Underwater Menace)
The Eleventh Doctor initially attributed Rory Williams's resurrection to a miracle. (TV: The Pandorica Opens)
The sudden end of death on Earth in 2011 became known as Miracle Day. (TV: The New World) When Oswald Danes saw Jack Harkness come back to life after Miracle Day ended, he thought it was a miracle. (TV: The Blood Line)
The inhabitants of Detrios named their new source of light and heat the Miracle. (PROSE: Head Games)
When Alistair Gryffen found that the chess room in Gryffen Manor was remarkably tidied up, he called it a "minor miracle". (TV: Black Hunger)
In 4202, the Fifteenth Doctor was disappointed when a ham and cheese toastie delivered to him in the Time Hotel from 30 minutes in the future was nevertheless microwaved, but Trev Simpkins told him he could not expect miracles. (TV: Joy to the World [+]Steven Moffat, Doctor Who Christmas Special 2024 (BBC One and Disney+, 2024).)
By the 59th century, human science had progressed so far that what were once thought of as miracles of religion, such as resurrection or walking on water, had become commonplace. (AUDIO: Blood on Santa's Claw)