Rat

Rats were small rodents found on Earth. They were generally considered pests by humans. Polly was virally incapacitated by her fear of rats in a 17th century jail, (TV: The Smugglers) and the Eleventh Doctor once claimed to hate rats. (TV: The Wedding of River Song) Rats were often associated with cheese. (TV: The Bells of Saint John)

History
According to folklore, the Pied Piper rid the German town of Hamelin of its rats in exchange for twenty bags of gold in 1284. (COMIC: Challenge of the Piper, TV: The Day of the Clown)

In 1605, the drains near the Houses of Parliament in London were infested with rats. The plotter Thomas Percy was disgusted by them. (GAME: The Gunpowder Plot)

In the 14th century, fleas on rats carried the bubonic plague throughout Europe. Terileptil prisoners who found themselves near London in 1666 exploited this to engineer a new plague variant that was injected into the rats. Plague was prevented by the Fifth Doctor. (TV: The Visitation)

In 18th century France, Susan was frightened by the rats she saw in the jail cell in which she and Barbara Wright were imprisoned. (TV: The Reign of Terror)

During the Spanish Civil War, the trenches were often infested with rats. George Orwell found them the most distressing factor of trench warfare. (PROSE: History 101)

While escaping the Squall in 1910, Amy Pond and Rory Williams entered the London sewers. The sewers were infested with rats, to Amy's horror. (PROSE: Paradox Lost)

In the 1970s, Arthur Linwood, a medical student with a morbid fear of rats, was killed at Stangmoor Prison when the Keller Machine turned his fear against him. His fear was so great that rat bites and scratches manifested on his face and neck. (TV: The Mind of Evil)

In the cellar of a Spanish hacienda in the 1980s, Shockeye of the Quawncing Grig caught a rat, broke its neck and began to devour it raw. He was displeased with the taste, hypothesising it might be more tolerable smoke-dried. (TV: The Two Doctors)

In the early 2000s, undercover Krillitane at Deffry Vale High School freeze-dried rats to eat later. (TV: School Reunion)

In 2050, the Space-Time Manipulator released a couple of black rats in Gryffen Manor, frightening Darius Pike. While these rats were otherwise identical to normal rats, they multiplied once every ten seconds. (TV: Liberation)

Following the 22nd century Dalek invasion, the rat population in England surged, likely because basic services had been discontinued. Prices for cats went through the roof. (PROSE: Legacy of the Daleks)

Paradise Towers had a rat population after it fell into ruin. (TV: Paradise Towers)

On an unnamed planet, the Gyros destroyed rats which tried to eat the food the robots had harvested and stored. (COMIC: The Gyros Injustice)

At some point in the 52nd century, rats would sneak into the Seventh Transept where they were eaten by the skulls of the headless monks. (TV: The Wedding of River Song)

Rats existed on Skaro until the latter stages of the Thousand Year War. (AUDIO: Davros, Corruption)

In experiments
Rats were used in experiments as test subjects, since they could be bred quickly. In the late 19th century, Magnus Greel created giant rats and set them loose in the London sewers to guard his underground laboratory. (TV: The Talons of Weng-Chiang)

Richard Harries used a pair of sibling rats in his experiments into shared brainwaves. The actions one rat learnt could be completed by the other through the process. The pair had a collective memory. Cuthbert Simpson implanted them with nano-cams and set them free, using them to watch the residents. After Simpson was blinded, he relied on the rats to allow him to see things and kept them on his person. (PROSE: The Banquo Legacy)

A lab rat was used by Owen Harper to demonstrate to the Torchwood 3 team the ultimately lethal effects of the "Sex Gas" on its host. The gas would cause the victim to explode, which proved to be no different with the rat. (TV: Day One)