The word canon has a literary meaning - in this context, a canon is a set of writing felt by someone to embody and exemplify the norms of those works which are non-canonical. An anti-canon is just a canon appointed by someone else to oppose a hegemonic canon.
In mathematics or informatics, a canonical form is a normative way of expressing or describing an object, so again, a norm created by a group to facilitate sharing of concepts.
In Superman comics, Star Wars books and so forth, "The Canon" refers to the fictional history which is considered (ostensibly by the publishers) as normative by the audience. Other histories may have taken place in alternate realities, parallel storylines and the like, but the canonical events are the ones which "actually" took place, and the chronology within which they are taken to have occurred. Fan fiction, for instance, is non-canonical.