Is it perverse to just quote the original inception by Crane?
An obvious nice collection would be the paper with Yetter on examples of Categorification.
However, I actually like another Paper of Yetter's better in this direction; categorical linear algebra.
Also, Rosenberg's Noncommutative spectrum is a categorification: pdf-link. Not in the strict sense, but "morally". That would be undoubtedly my favorite.