A tagged database, it seems to me, is pretty much the best way to organise and archive visual material. I think my position on it is similar to people who use Evergreen Note-taking and go on and on about how a directory is just fundamentally a bad data structure / organisation format for notes.
From memory I think Shimmie and Danbooru both implement image pooling and, as @darlene mentioned, parent-child relations (which are both great for things that are in some way connected to eachother, but without enough relevance or notability to constitute an entirely new tag). Many boorus also have an internal wiki, to collate tag information and best practices. It would be interesting to consider how we could integrate such a thing with the forum.