A canon is a body of work that is held to be 'true' or that 'really happened'. The concept of what is canonical often arises when a set of stories featuring the same characters or themes are written by multiple authors over a lengthy period of time.
The term derives from the Christian Church. There were hundreds of different Books. The early Christian Church agreed upon a set group of books that became the Bible. These books were said to be the canon, while the books excluded were said to be apocryphal. It should be noted that the Roman Catholic and Protestant churches have different ideas of what the canon is.
The term canon was later applied to the various stories featuring Sherlock Holmes. Holmes fans agreed that those stories written by Holmes' creator, Sir Arthur Conan Doyle, were canonical, while those written by others were not canonical.
In Science Fiction, as one example. Star Trek creator Gene Roddenberry proclaimed that all live action Star Trek television series and movies were canonical, while the animated series, the books, comics etc. Were not canonical.
No Doctor Who canon has ever been stated. In fact, various people who have worked on Doctor Who have actually mocked the idea of there being a Doctor Who canon.
However, certain people (and certain websites) have arrived at what is known as a "personal canon". That is their own personal ideas or beliefs on which stories "count", and which don't. People are free to have their own personal canon, as long as they don't try and force it on others.