Here's what I've "learned" with regard to tags. The UI needs to be effortless. I've encountered exactly one program that accomplished this. It was written over 10 years ago and has since been abandoned. It automatically generated a fairly sensible set of tags from context. Then the user could adjust. They were presented as a comma-separated list -- just edit the list, free-form. I had thousands of bookmarks, spanning…
The closest thing I'm aware of is KDE 4, but it's not using a special file system. I haven't used KDE 4 yet but it sounds like it's integrated into the overall desktop system, including Dolphin, the file manager.
It uses NEPOMUK (Networked Environment for Personal, Ontology-based Management of Unified Knowledge). Quick description from wiki: "NEPOMUK-KDE is featured as one of the newer technologies in KDE SC 4. It uses the RDF store Soprano and, on a technical level, allows associating metadata to various items present on a normal user's desktop such as files, bookmarks, e-mails, and calendar entries. Metadata can be arbitrary RDF; as of KDE 4, tagging is the most user-visible metadata application."
The KDE site for NEPOMUK looks like it has some good information: http://nepomuk.kde.org/
General NEPOMUK specifications: http://nepomuk.semanticdesktop.org/xwiki/bin/view/Main1/Deli...