@AAMy technique involves a lot of nesting to stay organized and although I've thought about a tag-based system the advantage of folder nesting is its compatibility with different operating systems.
My pony images folder could use some more organization, to be honest.
I find that different methods of organization are best when you have different numbers of files to keep track of. Folder nesting works good up to a point, but then it becomes more of a hassle to upkeep it than something like a tagged system. Right now, one of the issues keeping me from going right to a tagged system is that there doesn't seem to be an equivalent function to the galleries/pools function on the boorus. an ordered file collection for variant images or artist sets.
In Hydrus I kinda fixed the problem using "Parents" and "namespaces.
So it is like this:
Top parent: show:my little pony (namespace "show")
child: — character:applejack (namespace "character")
child: — gallery:015 (namespace "gallery")
child: — file01
So, in this way I can keep track of files and the order they have in the parent gallery. Granted, to do this manually is a real pain but I have no idea how to automatize this.
The search workflow for example, is to search for "applejack", then the gallery, and then look at the tags (01, 02, 03…) for their order. At this time I didn't figure out yet how play the files in an ordered fashion in the Hydrus' viewer. The developer says that this is doable and he's thinking how to do it.