I thought about this problem and explored the solution space but still fail to get a final answer. The problem with flat file storage is that the size of the directories grows very large making backups and browsing a pain. And the dbms solution has the disadvantage over beeing not browseable (using file system tools) and beeing a "black box" of sort.
Also I prefer solutions that are slick and do their job fast. That any alpha/beta projects are out of the question for a durable data store, is obvious IMHO.