It depends on the profile of the data and what logic you are going to be using to access it. If you simply need to save and fetch named nodes then a filesystem-based database may be faster and more efficient. (You could also have a look at Berkeley DB for that purpose.) If you need to do index-based searches, and especially if you need to join different sets of data based on keys, then an SQL database is your best bet.
I would just go with whatever solution seems the most natural for your application.