Stuff like this is cool, but it really points out just how poor the filesystem is for organizing certain types of data. The "Why does TMSU not detect file moves and renames?" question in the FAQ really highlights how this isn't helped along by the filesystem at all.
One comment mentioned BFS, which had some really cool stuff. There's an Ars Technica article that touches on some of it[0].
The secret to BFS, in my mind, is that applications use it. The Haiku Mail app, as noted in the article, used the filesystem as its email database by attaching its own attributes to messages. This is also an example used in the "Practical Filesystem Design with the Be Filesystem" book[1].
Unless the metadata becomes a first class citizen in the filesystem, any attempts to layer it on top will have problems. Either applications won't understand it or normal filesystem operations will cause the metadata database to become de-synced with the filesystem data.
[0] http://arstechnica.com/information-technology/2010/06/the-be...
[1] http://www.letterp.com/~dbg/practical-file-system-design.pdf...