It seems to me that directories are a fundamentally flawed system or organizing files. A natural way to start a directory structure is by basing it on the type of file (i e. games, music,
pictures etc) but that will quickly fall apart after you want your files of different "types" relating to X to be under the same directory. So now you can either create some symlink mess, include the wrong "type" of file in your directory tree, or restructure. The problem with restructuring is that it's a lot of work and the end result is not really worth it. What tends to happen (at least for me) is overly deep directory structures (and/or too much branching) that are tedious to navigate, and in the end have the same problem. Another option is to just bite the bullet and create a X subdir for each of your main directories that have relevant files for X which is what I do. But that really sucks and I wish there was a better alternative that actually worked with existing programs which assume a directory based organization. There are some alternatives that work on top of existing filesystems e.g. tag based systems but I haven't tried them yet and I suspect they have their own headaches.