You're aware of the application_id pragma? That's what this guy was created for: http://www.sqlite.org/pragma.html#pragma_application_id
e.g. It's like with photos (JPG) were you would only know it was shoot with a Canon camera, or a music file (MP3) that only stores the application name media player.
Most common file formats support metadata formarts like JPEG with its EXIV, ITPC, XMP and MP3 with ID3 v1 & v2, etc.
So for SQLite4 a very simple key value format would be great, with some predefined key-fields.