I thought there was an application that did something like this, but can't remember it anymore. It's nice to see a writeup that steps you incrementally through the benefits of this approach.
Acorn (awesome image editor for Mac) uses SQLite as .acorn image format.
Schema:
sqlite> .schema
CREATE TABLE image_attributes ( name text, value blob);
CREATE TABLE layers (id text, parent_id text, sequence
integer, uti text, name text, data blob);
CREATE TABLE layer_attributes ( id text, name text, value blob);
My app, Mémoires (diary for Mac), and some other Mac apps, use SQLite via Apple's Core Data as document format.