I use a folder/sub folder system. Basically, I have one folder that houses all the other files and folders for a specific mod. Within that folder are more folders that contain all the files for specific modules/areas. Within those folders are folders separating the types of files. So it looks a little like this:
Now occasionally the sub folders for files will have even more sub folders within them, the voice overs folder is a good example.
So yeah, I just organize everything into a bunch of sub folders within one big folder.