BNodes Out! discusses how any usefully scalable system doesn't use blank nodes. What is interesting is the comment on YADS (Yet Another DOI Service). The best reference is Tony's presentation although it is mentioned in Jane's as well. "YADS implements a simple, safe and predictable recursive data model for describing resource collections. The aim is to assist in programming complex resource descriptions across multiple applications and to foster interoperability between them...So, the YADS model makes extensive use of bNodes to manage hierarchies of “fat” resources - i.e. resource islands, a resource decorated with properties. The bNodes are only used as a mechanism for managing containment."
This sounds a lot like RDF molecules and supports visualization (apparently). This seems like a good use of molecules that I hadn't previously thought of (Tony's talk gives an example of the London underground). The main homepage of YADS isn't around anymore - it'll be interesting to see if it's still being used/worked on.
Update: Tony has fixed up the YADS home page (there's also an older version).