I think it's very important for everyone to organize their disks. But to a lot of people this is a daunting task. So i'm provide how I've kept my disks organized for almost 3 years now.

The first step is to create a Filesystem Hierachy Standard. If you use Unix regularly, you might be familiar with something like this. I think that every /home (or C:\Users for Windows users.) can benefit from having a written standard.

So first thing we want to do is ask ourselves: "What directories will I create, and what will be their purpose?". Let's start with an obvious example:
/home/USER/documents: This is a very simple one, what is this directory's purpose? Obviously it's to store documents. But let's go a step further, we need to categorize those documents. So under /documents, we can have /work, which obviously stores work documents, or /documents/ebooks, which stores e-books. At this point you should be getting the idea of how this will work.

Here, i'll provide an example FHS that you can use:

/
    /archives
        /youtube
        /backups
    /games
        /roms
            /gba
            /n64
            /wii
        /steamlibrary
        /gog
        /dos
    /documents
        /ebooks
        /work
        /financial
            /banking
            /mortgage
            /loans
        /documentation
    /programs
    /productivity
        /programming
        /video
        /audio
        /art
        /documents
    /multimedia
        /shows
        /anime
        /educational
        /music
        /videos
        /movies
    /misc
        /virtual-machines
        /unknown-files
    /temporary

This is just an example, and how this will look depends on the individual making it. But hopefully you get the idea behind it. And of course, as times goes, you'll probably be removing and adding directories as your interests come and go.

Anyways, I hope this helps people.