I agree that there's lots of value in the simplicity of a tree hierarchy as a default, but sometimes the extra power of a tagging/labeling system would be valuable. Essentially it gives you a generic graph structure. Others have mentioned that this is valuable for things like media, ie photos that often need to be members of multiple album collections. It could also have other benefits as well, such as being able to visualize your filesystem as a graph, and easily see clusters of data depending on which tags are used the most.

The only heuristic we really have for tree filesystems to get a feel for a subtree (child folder) is the total disk usage of that folder, or maybe total number of files in the subtree.