Prose stories first appeared in the inside covers of the first issue of Doctor Who Magazine, then known as Doctor Who Weekly, starting the Fourth Doctor. They continued in 1989-1980, 1986-1995, and then sporadically until the final story in 2005. A continuation of the first story, now staring the Twelfth Doctor, would appear to celebrate the magazine's 500th issue in 2016.
Miscellaneous illustrated short stories briefly appeared in the pages of Doctor Who Weekly from 1989-1980, starting the Fourth Doctor. They returned in 1986 and would appear sporadically afterwards — even during the run of short stories under the Brief Encounters umbrella — until 2005.
Starting in 1979, and having brief re-appearances in 2013 and in 2016, Doctor Who Magazine published in-character letters, being "written" by characters such as the Fourth Doctor and Peter Capaldi.
From 1990 to 1994, Doctor Who Magazine published illustrated short stories under the umbrella title of Brief Encounter. These stories focused on having Doctors and/or companions who had not been on screen together to meet each other. These stories were also published in Doctor Who Magazine specials and Doctor Who Yearbook
From 1992 to 1995, Doctor Who Magazine published exclusive illustrated preludes to upcoming Virgin New Adventures novels. More often than not, the stories did not include the Seventh Doctor, rather focusing on original characters in the novel or previous incarnations of the Doctor.