I use lots of nested sub-folders to organize files and I mirror the structures between the html file directories and the image directories.
Same with music files if the site has those.
Usually there aren't enough js files or includes for that to be an issue, so I usually just have one directory each for those.
I designed a site for a photographer earlier this year and I organized the files this way.
(lather, rinse repeat)
There are no more than 10 files in any given directory.
All the backgrounds are in one image sub-directory, cover images from his publications are in another and are further sorted into sub-directories by publication.