They're not really organized in any particular fashion on my end. Alphabetically would be the best way to put it, and they're usually not even stored in their own folders (or, if they're from a collection of WAV/AIFF files, they're just left in their original extracted folders). However, I do recycle samples from other modules I have made (I also make limited use of samples from other modules, but I mostly don't go for it), and lately if I have been exclusively using samples extracted from soundfonts as SNES samples, I put them in a leftover IT file that has the original loop point.
There are exceptions to this rule, though. Samples ripped from the SNES games are stored in a folder sorted by game and, depending on how the IDs are organized in the game itself and in the SPCs themselves, I may sort them out into "sets".