Is it a coincidence you framed the question in the same way as Houde and Hill did in their well known (in HCI) paper: What do Prototypes Prototype?
I think the scope of their paper is quite different than yours, but you might benefit from their aproach: creating a taxonomy of the role prototypes play in research.Such taxonomies do exist for the RtD aproach in HCI, but I do not know of a specific computer science one.
Houde, S. and Hill, C., 1997. What do prototypes prototype. Handbook of human-computer interaction, 2, pp.367-381.