I made a folder that I call BASE MODS for all of my must-have mods + defaults with a small amount of CC that I use all the time. Each save file has it's own game folder so I can swap them out. I add the base mods folder and then only install extra content as I need it for that save.This means things load slightly faster and I don't get lost looking for things in the catalogs. My entire CC collection and store collection is archived with pictures separately on a storage drive to pull from if I need anything else.
The downside is this takes up drive space so I grabbed an external drive on sale for general backups, archived content, extra saves, and exported NRaas settings. The only sims3packs I install are store stuff, worlds, and sims. The rest gets converted to package file. The great thing about package files is you can merge them, unlike sims3pack. The launcher becomes funky when you install too much through it.
I'm still fine-tuning how I organize things... My CC/Mods are organized by Modify (Mods), Defaults, Patterns, Poses, Sliders, CC (Individual creators), and Maternity (Maternity enabled clothing). My store content is backed up & organized by Worlds, Sets, Venues, Premium Content, and Individual items.