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A soul was an ill-defined, sometimes religious term for the essence of a sentient being. For some, it was closely tied to the definition of life. According to the Eleventh Doctor, souls were made of stories, not atoms. (TV: The Rings of Akhaten) The soul was sometimes synonymous with a person's mind, their soul being composed of their memories, but even this was not considered accurate. However, the removal of a person's mind to another plane could simulate death, leading to the allusion between a soul and a mind. (PROSE: Timewyrm: Revelation, Falls the Shadow)
The souls of the dead passed through the Moon's influence on their way to Heaven, where they were sometimes caught by the Lunaries and offered new bodies. Leonardo da Vinci and Roger Bacon were two such persons who accepted, and by 1590 were still living there. (PROSE: Minions of the Moon)
In the 22nd century, some artists used soul extractors to improve their art, literally extracting portions of their souls and inserting them into the canvas. They used it sparingly, as the results of over-use were lethal. One time when an artist became addicted, he created a living being within the canvas. (PROSE: Untitled)
Death, or Duroc, attempted to collect thirteen souls in order to fully enter our reality. He was stopped by Owen Harper at twelve. (TV: Dead Man Walking)
The neutron eaters tricked Oliver Harrington into bringing more of them through from their dimension by making him think that angels were souls, returning from Heaven to the mortal world. (AUDIO: Lost Souls)
In 2013, Miss Kizlet scavenged the Wi-Fi to upload the souls of humans to feed to her client. (TV: The Bells of Saint John)
Astral projection was a method of travel in which the soul was separated from the body. (TV: Image of the Fendahl)
Souls in culture
Human
The Soulless were a group that arose during the Miracle Day event, which had rendered virtually all humans on Earth incapable of dying. Members of the Soulless believed that because they could not die, they had been robbed of their souls. (TV: Dead of Night)
Gallifreyan
The Time Lords had a rite called Soul Catching, in which a dying Time Lord would transfer his soul to another Time Lord, which would then get assimilated into the Matrix. (PROSE: The Devil Goblins from Neptune)
The Eighth Doctor claimed that if he looked into the Eye of Harmony, his soul would be destroyed, and the Bruce Master would be able to take over his body. (TV: Doctor Who)
Aplan
The Aplans believed that, after death, their souls ascended through six levels to their version of the afterlife. They dedicated Mortaria to this. (TV: The Time of Angels)
Dalek
According to Rusty, the Daleks didn't have souls. (TV: Into the Dalek)
References
Blon looks into the "soul" of the Doctor's TARDIS. (TV: Boom Town)
The Qetesh, a species that fed off of the excitement of others, were sometimes referred to as "soul-stealers." (TV: Goodbye, Sarah Jane Smith)
The Ninth Doctor said that the Heart of the TARDIS was its soul. (TV: Boom Town)
The Lupine Wavelength Haemovariform took a human Host, saying that he "carved out his soul and sat in his heart". (TV: Tooth and Claw)
When he revealed that the Krillitanes needed children rather than adults to unlock the Skasis Paradigm because of their imagination, the Tenth Doctor said that they were using their souls as well as their minds to crack the code. (TV: School Reunion)
Having deactivated the emotional inhibitors of the Cybermen, which resulted in their deaths, the Doctor told the Cyber-Controller that he had gave them back their souls. (TV: The Age of Steel)
Captain Jack Harkness claimed that technobabble was good for the soul. (TV: Day One)
After Amy Pond looked directly into the eyes of a Weeping Angel, the Eleventh Doctor described her as having "opened her soul to it." (TV: The Time of Angels)
When the Twelfth Doctor linked his mind with Rusty's, Rusty claimed to see into the Doctor's soul and saw "beauty", "divinity" and the Doctor's "hatred of the Daleks" and saw that "it [was] good". (TV: Into the Dalek)