What does the classifying space of a category classify?

Ieke Moerdijk has written a small Springer Lecture Notes tome addressing this question:"Classifying Spaces and Classifying Topoi" SLNM 1616.

Roughly the answer is: A $G$-bundle is a map whose fibers have a $G$-action, i.e. are $G$-sets (if they are discrete), i.e. they are functors from $G$ seen as a category to $\mathsf{Sets}$. Likewise a $\mathcal C$-bundle for a category $\mathcal C$ is a map whose fibers are functors from $\mathcal C$ to $\mathsf{Sets}$, or, if you want, a disjoint union of sets (one for each object of $\mathcal C$) and an action by the morphisms of $\mathcal C$ — a morphism $A \to B$ in $\mathcal C$ takes elements of the set corresponding to $A$ to elements of the set corresponding to $B$.

There is a completely analogous version for topological categories also.

It's one level up the categorical ladder, but you may find this paper interesting:

http://arxiv.org/abs/math/0612549
Two-Categorical Bundles and Their Classifying Spaces
Authors: Nils. A. Baas, Marcel Bokstedt, Tore August Kro