The term 'canonical' is very general and any attempt to create a "precise notion" may be questioned and can never be proved as such. However, there is a canonical candidate, which at least concerns canonical morphisms for constructs and other structured sets, which has a clear logical character.
First, every mathematical structure on a set is determined by relations between sets. For group structures there is a primary relation $r$ that is a function $G\times G \overset {r}\longrightarrow G$, $(x,y)\underline{r} z \Leftrightarrow z=x\centerdot y$ and some secondary relations which are conditions on $r$ (associativity, unit element and inverses). For a topological space the primary relation could be $2^X \overset{r}\longrightarrow X$, where $2^X$ is the set of all subsets of $X$ and $M\underline{r}x$ is the relation $x\in \bar{M}$ (the closure of $M$).
Whenever the main relation of a mathematical structure is given on the form $F(X)\rightarrow X$, for a functor $F$ in the category Rel (where sets are objects and binary relations are morphisms) which maps morphisms $X\overset {f}\longrightarrow Y$ on $F(X)\overset {F(f)}\longrightarrow F(Y)$, it is possible to define morphisms between the structures as (in general non commuting) diagrams:
$\require{AMScd}$
\begin{CD}
F(X) @>F(f)>> F(Y)\\
@VrV V @VVsV\\
X @>>f> Y
\end{CD}
such that
(1) $\quad \rho\underline{F(f)}\sigma \Rightarrow (\rho\underline{r}x\Rightarrow\sigma\underline{s}f(x))$.
This condition on $f$ gives the canonical morphisms to every construct that provide canonical morphisms.
Example: If $F$ is the (contravariant) functor defined as $2^X\overset{2^f}\longrightarrow 2^Y$, where $M\underline{2^f}M'\Leftrightarrow M=f^{-1}(M')$ and $r,s$ are defined as
above, then due to (1):
$M=f^{-1}(M')\Rightarrow (x\in \bar{M}\Rightarrow f(x)\in \bar{M}')$, so $x\in \overline{f^{-1}(M')}\Rightarrow f(x)\in \bar{M}'$. (Continuity).
Thus, in Francois's example with the shoes, unless we're told which shoe is left and which is right (which is just like having distinguished points), there's no actual way of distinguishing the two shoes. Maybe "logical way" or "distinguishing" isn't the right phrase?
– David Corwin Jun 15 '12 at 05:42