My home directory is a shared drive with:
~/Backup/...
Just random things I needed to backup from somewhere else, stuff like my wifi router config files ends up here, or images of my phones
~/Code//...
This is mostly source code I wrote organized by project
~/Docs//...
These are documents (mostly PDFs) organized by category, e.g. "History", "Manuals", "Datasheets", etc... Some documents are further grouped inside these
~/MyDocs/...
These are documents I've generated myself, this is pretty flat, the only further organization inside is taxes//...
~/Images/...
~/Images/backgrounds/...
These are mostly images I've found online, images that would make good backgrounds are copied into backgrounds. Some of my machines pick desktop backgrounds automatically from there
~/Movies//
These are movies made by other people
~/Music///...
Music made by other people
~/Photos//...
These are photos I've taken, organized by device and date
~/Temp/...
Temporary files, theoretically this gets emptied out, realistically I haven't run out of space yet
~/Videos/...
~/Videos//...
~/Videos//...
Parts of various video projects I've worked on. Source material organized by device and date, bits for specific projects organized thus
~/VMs/...
Images and state for various virtual machines
The home directory has a few other subfolders dedicated to important or ongoing projects, for instance each of my kids has a folder, as does the house I'm designing. The home directory also accrues a good amount of other random files, often prefixed with some useful grouping id and an underscore. I try to gather these up or delete them from time to time when it starts to feel cluttered. A few files are mainstays. I also have a few dotfolders for things I want to configure the same on different machines.
On my individual machines I usually link ~/Downloads and ~/Share to local storage. My general rule is to always copy files from Downloads, leaving the original file intact. Thus the Downloads directory acts as a historical archive of everything I've ever downloaded on a machine. The Share folder contains copies of files I'd like to share with the world. I use this folder when configuring p2p filesharing services.
I let the OS manage the rest of the hard drive however it sees fit. If I'm using a system that allows me to put files on the desktop I try to refrain from doing so, but occasionally I'll use the desktop as a temporary space.