I store most my files in ~/Documents. I have among other various folders a folder dedicated to code, to pdf books and to my school work as well as work. My code folder is separated by language and in each language folder I have a folder named bins which holds various one off experiments. Within each language folder I also have various long standing projects and such. My school work is separated by semester and then within those by course Identifier. My pdf books are separated by topic. Usually I tend to nest things in somewhat deep hierarchies. I can still quickly navigate by terminal because I use z.sh [1].

[1]: https://github.com/rupa/z/