The only good reason not to use a relational database is that they suck at modeling complex entities and their relationships. Shattering nice entities into small relations to get them normalized, adding join tables to model many to many relationships and all that fun. Everything that is not roughly tree-like is just painful.
More than once I finally decided to just stuff the really complex pieces into a blob - XML or what ever worked best - and just deal with it at the application layer. Not pretty, not fun, but still less painful than modeling and dealing with it in the relational model.