Use standard office procedure, basically. Stuff comes 'in', and gets filed away constantly.
You have an 'in' tray, with me it's my 'Downloads' folder. Even locally-generated files get put there. So stuff comes into that and it rapidly gets full so stuff then is forced to be put elsewhere.
Have an 'archive' partition which is really a 'write-once keep-forever' partition. So stuff that you want to keep gets put there, your music, your photos, your video, your ebooks, etc. You get the idea. Tree-structured so you can find stuff easily.
Your home folder is where you keep the really important stuff like documents. They go in a 'Documents' folder, which is also tree-structured. In your home folder you might also keep your current work-projects. But that is just about all that you keep close by. You don't need to keep all sorts of extraneous shit in your home folder. Get some discipline to move stuff out of your home folder as a constant policy.
This means that there is stuff that you want to keep and stuff you don't. Delete that stuff you don't want to keep. It only clutters up your life. Archive the good stuff on that 'write-once keep-forever' partition.
I also make an index of all files on the computer twice a day. To find a file you search the index, not rummage haphazardly through folders.
Last thing: backup your whole computer at least once a day. By reducing your home folder to just essentials you can make a snapshot of it on a daily basis. My snapshots are between 10 and 15 gig. Any larger and I investigate what's taking up all the space.
The archive disk can be backed up within a few minutes, because there is very little change day-by-day and it only takes a moment to back up those few changes.
If all this seems a lot of work, it isn't really. Most of it is automated with a small bunch of 'cron' jobs. My main job is deciding what is keepable and what isn't. And where it belongs.