The axioms of category theory arise in many contexts
structures and maps between them
structures and interpretations between them
theories and interpretations between them
theories and proofs between them
states and processes between them
words (as input/output) and programs (automata, algorithms) "between" them
points in a geometric space and paths between them (→ Feynman's path integrals?)
structures representing other structures, i.e. with representations between them (representation not only in the representation theoretic sense, but in a more general one)
I am looking for more examples of this kind.