By author? By website? By character? By rating (sfw/nsfw)? etc?
I put stages in 1 flash motions in another and models in another flash drive and all in an external 6tb hd
I generally do it by category.
Each of the character models I possess/made have their own folder within my main models-folder, including models that have outfits rigged to them. But I organize my stages, unrigged clothing, and items (accessories from vehicles, hand-held items, and other things) into their own sub-folders within the main models-folder.
And also in my stages folder, I got another sub-folder I labeled "various stages" to keep my favorite stages separate from the ones I'm not too worried about losing in worse-case scenario.
And I keep my MMD stuff backed up onto separate flash drives (as well as everything else). I remove some things I don't care too much about when updating my backups (such as wav files because they're easy to replace), the various stages folder, and other things I'm not worried about.
I recently thought about getting an external hard-drive for more back-up than the typical flash-drives. My philosophy; there's no such thing as "too much back-up" when it comes to data.
At the top level, I have folders for models, motions, dances, and stages. My stages... I don't have very many, so that's just a disorganized pile. The models I have are mostly grouped by franchise (Fate, Kawaii Strike, Arknights, RWBY, Vocaloid, Touhou, Xenoblade) but I also have folders that sort models by the creators (Quappa El, J&J, Kakomiki) and a Vtubers folder. Then I have a long list of one-off models; no sense making a subfolder unless I have 4 or more models that share something. Honestly the biggest tip I can give you is to rename the folder of each specific model in whatever way makes sense to you, adding tags like creator or warez or sfw, or just converting the JP characters to english stuff. My Vocaloid folder is massive so I've renamed each folder to have the character's name first (Miku/Rin/Gumi/etc), that keeps things sufficiently organized.
i put most of my R-18 stuff in the Wave sections, because i dont store .WAV files there as because I store .WAV files with their respective motion instead. i have this "Effects" folder where i store certain effects, and also when it comes to organizing stages or models i normally put it in a folder with the creator's name if i downloaded multiple files from a certain creator. if i haven't, ill just put it in an "Other" folder.
/lady confused face: you guys sort them? I have so few stage and model that I often use. I think naming the folder by the model's name is the most sufficient way. Stages likewise. Or maybe you can rename the stage folders for easy memory.
I have two folders: Comps and Resources. Comps is videos, both stuff in production (including timing notes) and full-resolution copies of finished work. Inside Resources I have folders named Effects, Models, Motions, Poses and Stages. Effects is MME stuff - Ray-MMD, PowerDOF, AutoLuminous, etc. Models is what it sounds like, each model in its own folder. Motions is sorted into one- and two-person dances, and each dance includes the associated song file and all motion files. Poses is the handful of pose files I have, though I don't think I've actually used them for anything. Stages is split between indoor and outdoor stages, again with each stage in its own folder.