Tracker which I have designed as a replacement for Gnome's Medusa is coming along nicely (about half complete). Once complete it should make it easier to provide support for things like VFolders for GnomeVFS as well as a generic metadata store for all files/apps and especially Nautilus.
Tracker implements the File Metadata spec which I designed to cover all the basic metadata needs. I am hopeful I will soon be able to leapfrog both OS/X spotlight and Vista in this department with support for fist class documents too (emails, conversations etc).