We have five subject areas, so we have five subfolders within that main folder. Each subject area subfolder contains videos for multiple courses. Right now we have a manageable number of videos in each subfolder so searching and trying to name things clearly is sufficient for us to find things. We just started this subfolder setup so we may decide to do a course-based subfolder structure in the future. It would be great to have sub-subfolders so we could have the subject subfolders with course sub-subfolders within, but that does not appear to be a feature available.

I have mine organized by our products, which match the tags we use in TI. When I update a video, I put the date of the update in the file name in Wistia. It makes it easy to see when it was updated. I also make sure to accurately name the videos there so I can quickly search for them. 

I also have an Archived folder so I can keep the data for things we no longer use in TI..not a lot, because I usually just replace the video to update it, but there are a few that I keep.