Here are some variants that I've seen so far.
Careful people that are afraid to spoil the system use:
Crazy people have always an original place to hide files in:
Linux distributions put files according to the Filesystem Hierarchy Standard.
Some years ago I belonged to the first group and I was putting everything into
/usr/local to be sure that there is just my stuff. Today I belong to the second one... I use
/data for my laptop. Which is not so great idea, but it is my laptop and no one ever will have to (won't even be able) to touch it, so it is my mess. Some of the other ones like
/usr/local64 I have to use at $work, because it is ops decision or a historical reason (sniff, sniff).
I hope one day I'll further evolve to work according to the standards. Tiding-up my mess would be the easy part of the journey...