I use it in a network video recorder. https://github.com/scottlamb/moonfire-nvr/blob/master/design...
Data in a flat file would be much less efficient, and a SQL server (eg PostgreSQL) would be more for the administrator to deal with. SQLite's a nice sweet spot.
I've thought about using a key/value database (either a BTree one like SQLite uses under the hood or a LSM one like RocksDB). It'd be faster and less total code. But SQLite's too convenient to give up. The SQL interface is nice for debugging in particular. And it's already plenty fast enough, so my time's better spent adding some glaring missing features and better UI.