Vienna Content - where I allow the Vienna instruments to store themselves in their default folder structure
Player Instrument Content -where I allow NI powered instruments (and others, such as KongAudio stuff) to dump their libraries.
within the Kontakt folder I have this tree structure
Going further in, it depends very much what libraries I've got. I like a lack of clutter, so where a folder gets complicated I start looking to subdivide it again.
For instance, under Africa I have folders for percussion, strings, vocals and wind. Inside Percussion I have folders for Drums, Bells, Shakers, Snaps and Tuned Percussion. Inside Drums I've had to divide into Frame Drums, Talking Drums, Floor Drums, Bass Drums and Other. Whereas under British Isles I just have one folder for percussion.
When you get to the final folder I generally try to have all the NKIs at the top level, and bundle all their samples together in a folder labelled 'samples.' Just occasionally this isn't possible, either because an instrument comes split into 20+ NKIs for its various articulations, or because there's going to be a conflict of sample names. In which case I have separate folders for the instruments from different developers.
I've spent a lot of time getting everything to fit into this structure. I converted everything that I could from other formats. And where I have a library that has instruments in several of my categories I took time to move all the samples into the right folder, then resave the instruments so they new where to find the samples. For instance I split up the wind instruments in Anthology so that I can find them in their appropriate countries.