I've had good luck using sqlite3 for both a hobby project (a photo organizer <a href="http://github.com/kghose/Chhobi" rel="nofollow">http://github.com/kghose/Chhobi</a>) as well as for work (neural data analysis)
MongoDB is 'lightweight' in the sense it's easy to setup and persistence of both simple and complex objects is a breeze. The query interface is a bit ugly but it may be worth a look.