What is the perfect and ultimate parition and folder structure?

Show us your tagged file system implementation. What operating systems are supported?

Do you store program installers/archives/packages in one directory divided by category, or do you store them together with all kinds of other files which share a common subject (in other words, would you store a GIMP installation package in installers\graphics, or graphics\installers)?

I don't know what you meant by installers/archives/packages
do you mean Program Files? or the .exe installer?

I use my package manager.

Installers or achives (if the program doesn't need to be installed). But it's a conceptual thing really and program installers were just an example. I might as well ask if you keep all PDFs together and then sorted by subject, or if you put PDFs toghether with other files on a given subject.

Which thread?

Everything in one flat folder. Hierarchies are a form of oppression that you have been conditioned to accept. They are not ok.

That's more like retard level. Noob level would be to store shit in the built-in "Muh Documents" folder (where all sorts of programs love to take a dump in and create their own folders).

I put PDFs into subject/projects first.
CP/how to fuck a loli.pdf
Terr*rism/how to blow up federal building.pdf

storing all pdfs into one folder and then subfolders by subjects would be stupid. Files related to project could be of many types, pdfs, txt, mp4 etc. Why should you be required to visit 10 folders just to get files related to your project?

And if you needed to just look at list of all your pdfs you can just make a search on your HDD for *.pdf

This is simple.
At most 4 partitions for the OS. One for core functionality, one for all installed programs, and one for temp/swap
As long as the core partition remains, the system is usable, and there won't be an issue with full partition errors. Ideally, the core OS would be a read only partition that's only remounted read-write for updating, patching, or modifying.
User data gets it's own partition.

From there, you use some sort of logical disk management that allows for you to easily modify, add, and remove partitions for specific tasks. The disk manager should be able to do any one of these tasks with a single line, single command
One for media, one for games, one for VMs, one for special stuff, etc.