Vague definition of canonical:
Let $X$ and $Y$ be collections (often sets) for which assumptions has been made (has been given structures and/or are related somehow). A function $f\colon X \to Y$ is canonical if it is given by a rule using only the already given structure.
This explains the relation to the greek word rule (kanon). The precise meaning of the above are open for enterpretation: how much structure can the rule itself contain (maybe this can be made precise)! This "definition" somewhat contradicts many of the other answers, which for some reason is under the impression that canonical implies unique (or almost unique), which in my point of view is very wrong since different rules may define different maps. E.g. if we let $X$ be the objects in the category of abelian groups and $Y$ the morphisms then the definitions makes all the group homomorphisms $A \to A$ given by multiplication with an element in $\mathbb{Z}$ canonical, which to me is not a problem.
Usually when there is an especially simple rule it is often assumed without mentioning that this is the rule defining the function. E.g. most will understand the following:"there is a canonical endemorphism of any object in a category". This emphasizes the multiplication with 1 above as somehow speciel or "more canonical" than the rest. This is simply because the rule works in much greater generality and is shorter.
Usually if a rule is very simple the function will have nice properties. E.g. simply rules in category theory often define functors, natural transformations, e.t.c. This leeds many people to confuse the notion of canonical with "something behaving nicely".
I am somewhat puzzled by the use of the word uniform in one of the answers. The nature of the word uniform is "of the same form" and relates more to symmetries and things looking the same every where. This often leeds to canonical maps, since a choice at one point can sometimes be extended to a choice at every point. Please someone comment on this since maybe this is just a use of the word I have not seen before!
