My favorite example of this is Audacity, which stores their entire project file, including all the audio data, as a SQLite database. It's really amazing, you can stream audio data from many input sources into a SQLite database at once, it wont break a sweat, it's flexible and extremely safe from data loss due to crashes or power outages. As well as trivially mutable: many of these kinds of formats the "export" is a heavy-duty operation which serializes everything to JSON or whatever. But in SQLite, it's just a question of updating the database with normal INSERTs, very cheap and simple operations. We've put a similar system into production, and it's incredible how well it works.