Yes, for example I have made a folder of the 'base' plug ins that I have in the plug-ins folder (this makes it easy to see what is added / modified when installing new plug-ins or applying a cs upgrade) but leave the stereo and surround desks at the top level so it is easy to see which versions are being used. In plug-ins unused I have created folders eg 'Waves' - for the multiplicity of WavesShells and SoundToys installs create their own folder, and can just drag the complete folders, as required, into the plug-ins folder. Plug-in maintenance becomes a little more fiddly as upgrades won't automatically replace older versions of plug ins that are in folders. You need to do this manually. A small word of warning though, I believe there is a maximum depth of nested folders you are allowed to have in OSX.