I've thought about this a lot because I would like to keep things for a long time without it getting a mess. Since I started using Linux as my main OS six years ago, I had the chance to rethink my structure and this one still holds up through multiple reinstalls and studies/companies:
~/p/$projectname for bigger projects
~/p/$language/$projectname because there is usually
one obvious language to use for a given project
~/d/$school/$subject_code for current subjects
~/d/$school/$year/$subject_code for previous subjects
~/d/$company/ documents related to the company, such
as a contract, correspondence, or just work
documents. In most cases I get a company laptop,
so then this folder is really small.
~/d/archive/$year/($school or $company) for old things
~/d/private/$YYYY-MM-DD-description can be either a
file (such as 2019-01-01-Microsoft-support-call)
or a folder (2019-01-Microsoft-support-case)
~/d/private/finances/ is one of a few special folders
that do not use the time-based prefix. Other files
include a passport-style picture, encrypted copy
of passport, a folder containing my CV, etc.
~/Music a few things that are not on Spotify and
audio book archive (I don't trust Audible to keep
my library available as mp3 indefinitely).
~/Videos similar to Music but for videos
~/tmp/rm-me-on-YYYY-MM-DD files/folders which would
previously clutter my desktop indefinitely, but
which should survive a reboot (otherwise, /tmp)
~/bin/ user applications
~/bin/pf/ program files for ~/bin
Unsolved problems:
~/Downloads is a huge mess. I've been thinking of symlinking this to /tmp to
force myself to move out what I want to keep, but did not get around to it, so I don't know whether it's a good solution.
Programs put files in random places, mostly dot folders in my home directory
such as ~/.gnupg. This causes the following:
~/old-ssd still contains files from my previous SSD, and I'm not sure how to
decide which ones to keep. Every few months, I dig something up from there, so
it's definitely not ready to be thrown away despite having copied the
aforementioned folders.