My way is to have folders for each drum hit, and each sample. Each one is named to match the other sounds, so in KICKS I would have 040, and in SNARE 040, HATS 040, then in OTHER (main sample used) 040piano, 040strings. Then I also take it further by having 040b_strings if I have more than 1 set of strings for that track.
Pretty basic organizing, but even for me it gets out of hand sometimes and becomes a real mess because I'm in such a rush to start a track so that I don't lose my creative edge!