Canon
Canon refers to the works within a franchise that are considered to be "official" by its author, rights holders and fans.
Overview
The term "canon" originates in religious circles, where it was used to deem which Biblical texts were considered legitimate: for example, Orthodox Judaism considers the Old Testament of the Bible to be canonical, and the New Testament as "non-canon". The term was first used (albeit in a tongue in cheek way) in a fandom context by the fanbase of Sir Arthur Conan Doyle, to distinguish between the Sherlock Holmes stories written by Doyle himself, and those written by others. Some franchises take a stricter approach to canon than others, but since one work of fiction is no more "real" than another, it is up to the author or rights holders to decide which stories belong to their official continuity.
In Zoids fandom, which works are considered to be canonical has been a source of strife among the community. Each work of fiction in the Zoids franchise is generally set in its own continuity, many of which contain irreconcilable contradictions. Therefore, each work in the franchise is canon to itself, but non-canon to the rest of the franchise. For example, the Chaotic Century anime and New Century anime are canon to each other, whereas the Chaotic Century manga and New Century manga are non-canon to the anime or each other, the former being a Battle Story spinoff (itself non-canon to the second half of the Battle Story) and the latter being a standalone work.
The flipside to canon is Fanon, which are unofficial ideas that are commonly accepted as truth by the fandom (such as the Descendant Theory.)