I've played around with RDF/N3 databases a bit, but mostly then from a document-oriented storage angle. I believe this has much of what you're looking for, ie getting away from table-based databases, and moving closer to optimal data architectures.
Also, if you're curious about this sort of database design, NASA shared some interesting work on XDF: TheExtensible Data Format Based on XML Concepts[0][1], which was part of their long-range Constellation Project[2] toolset for building, launching, and operating the Ares spacecraft. They detailed it in this NExIOM slideshow[3], which reading again after quite a while brings back some very good memories. Enjoy!