I have brought this idea forward a few times when speaking with support. It would be extemely effective in organizing templates and media files. The more content that gets added into the system, the more difficult it is to find what you are looking for.
In addition to this, when selecting a template to use, right now you can search for a template through all the templates you have. If there was an (optional) folder field that would allow you to drill down the folder and respective sub-folder, so the templates list is only propigating the templates contained there - that would just make finding things worlds easier.
Similar to the above, having folders within folders for media that could be collected into sub-folders and searched in a similar fashion would make finding media files sooo much easier.