On the filesystem, I'm thinking of some sort of (possibly virtual?) document filesystem structured by:
* Title
* Author
* Subject
* Date
* Other?
The problem with a fixed / structured filesystem is that it's largely inflexible. The next option would be to have some sort of hybrid -- a persistent data store plus, say, hardlinks or symlinks onto that store based on other elements, could work, but would be somewhat annoying to maintain (though not impossible, and a tools-based approach might well work).
The advantage to a filesystem-based approach is that you'd be able to use any filesystem-based tools on it: find, grep, ls, cd, etc.
This also points to the distinct limitations of filesystems and naming conventions for document-oriented systems, generally. They're OK for statically-defined computer systems. Sometimes (/proc, /sys, /dev, /dbus, ... are all exceptions for which virtualising the filesystem is a current fix), but when it comes to the human realm, the oversimplification and reliance on standards creates pain.
A related problem is: how do you identify a given work, reasonably uniquely and reasonably persistently across variants?
Taking a content hash works for git, but doesn't apply particularly well to a human-readable document where whitespace, casing, characterset, character substitutions (straight vs. curly quotes, "-" and "--" vs. en and em dash, etc.), translations, multiple output formats, etc., might all create unique (and unrelatable) hash fingerprints.
In catologues, some tuple of author, title, and publication date generally suffices, and creates the general outline of a unique, but relatable, identity foundation. A book might have multiple editions or publishers, or multiple formats (ISDN relates these to the core work). Sub-parts (a chapter or section) might be included into other works. Etc.
I'd really like to have the option, say, of creating and relating:
* The source document.
* Some standardised markup (Markdown, LaTeX, some BDSM HTML5 or similar format, etc.).
* Generated outputs (PDF, PS, ePub, DJVU, Mobi, ASCII, etc.)
* Metadata: Author, title, publisher, publication, date, URL, language, various identifiers (LoCCN, ISBN, DOI, ...), etc., subject(s), rating(s), review(s), citation(s).
For research, this could be highly invaluable.