Practically every story that covers the Doctor Who universe takes place between two other stories. This is covered on story article pages under the 'Timeline' subheading. In this section information is placed that suggests why that story occurs between the two stories stated.
There are several sites that are often cited such as Doctor Who Reference Guide and Doctor Who - The Complete Adventures, however both "cheat" with stories that are difficult to place due to hard to define time periods during the Doctor's life or when not enough information is given in the story.
Other often cited sites are Wikipedia's Chronology of the Doctor Who universe and Lance Parkin's AHistory, which both, rather than organising stories by when they take place in relation to other stories they arrange stories into a timeline from "beginning" to "end" (or the start or the universe to its end).
During the 1990s and early 2000s when novels were published of Doctor Who stories by Virgin Publishing and BBC Books the Virgin Missing Adventures and Past Doctor Adventures had on the back of the books, under the blurb a statement that read "This novel takes place between STORY X and STORY Y", therefore allowing the reader to place where these stories took place.
Later Big Finish Productions also added indications for listeners where their audio stories took place in relation to other stories they had published.
A further theory sometimes subscribed to is using the broadcast or production order of stories as a method of ordering the stories, however with modern production methods where stories are recorded and produced in "blocks" this form of ordering can be extremely problematic.
On this wikiEdit
On this wiki, information from the back cover and inner covers of novels and audio stories is used as well as narrative indications from the stories themselves to indicate the stories that occur before and after the story on which the information is.