In $\mathbf{Set}^\text{op}$, $\hom(X, Y)$ is the set of all functions from $Y$ to $X$.
That said, there is an equivalent description: that $\hom(X,Y)$ is the set of all functions $\mathcal{P}(X) \to \mathcal{P}(Y)$ that preserve unions and intersections.
More precisely, $\mathbf{Set}^\text{op}$ is equivalent to the category whose objects are complete atomic boolean algebras and whose morphisms are functions that preserve all unions and intersections.
The bijection between the two descriptions associates to a function $f : Y \to X$ the function $f^* : \mathcal{P}(X) \to \mathcal{P}(Y)$ defined by
$$f^*(S) = \{ y \in Y \mid f(y) \in S \} $$
It may be interesting to note that there are naturally occurring categories where morphisms involve functions going the "wrong way". For example, in Top, the category of topological spaces and continuous maps, the homomorphisms $(|X|, \mathcal{S}) \to (|Y|, \mathcal{T})$ involve functions $|X| \to |Y|$ (i.e. a mapping on points) and also functions $\mathcal{T} \to \mathcal{S}$ (the inverse image of an open set is open).
A related notion is that of a locale. It's like a topological space, but without the set of points: a locale is just the frame of open 'sets'. So, in the category Loc of locales, a locale morphism $\mathcal{S} \to \mathcal{T}$ is a (structure preserving) function $\mathcal{T} \to \mathcal{S}$!