What is the best way to organize my videos and music files?

I have finished working on over (100) movies so far and have all my TV show episodes done so far.

Here is how I have my movies so far. All of my anime shows are in a folder called anime and each anime has its own folder which is the name of the anime.

Next I have all my cartoon or cartoon based movies in a folder called "Animated Movies" and then I just have one called "Movies". How would I go by better organizing these movies.

Should I sort them into genre titles based on what genre title is used first. Or should I make a folder for each genre and look them up online and see the main genre for each movie.

What Is the best way to do this.
Please help plus I have not gotten started with my music files yet ether.

The file system allows just one access path to the files.
But as you found out each medium has its own properties and it would be best to access in various, flexible ways.
So if you have to rely only on the file system's tree-like hierarchie, you are now at a loss as the way that seems best under certain conditions is not at all the best under different conditions.
The only way out would be a management program plus metadata in the files ("tags") that allows to arrange titles by different criteria.
For such a way the structure in the file system is completely irrelevant.
But as you have to save the files somewhere ... I would take care that files that belong together can be grabbed in one go, e.g. to create a zip archive or to copy them easily to a portable storage.
In this respect it does not make much sense to use criteria that are outside the influence of the actual artist like genre and create an access tree by these. Such an order will cause problems with music files as then tracks from a single medium will be spread all over the access tree and it will be hard to reconstruct the original shipment.

And even though I have uttered my preferences, it is still up to you and your use-case how you do it. And I bet there will be loads of other ways to get the individual optimum.
And if you want to get a flexible optimum, then the only way would be tag data in all the files.
Otherwise it means: there is no "best" way.

As @ohrenkino says, everyone has different needs, and there is no right or wrong. How you use your music, how you play your music, how you access your music--all of that can help determine how you store your music.

Here's me: I keep all my music in four folders:
Artists
Mixes
Soundtracks
Classical

Mixes & Soundtracks have a folder for each album. No sub-folders beyond that.

Classical has a sub-folder for each composer, with folders under that for each album.

Artists has a sub-folder for each artist, and a folder under that for each album.

It helps me keep it all organized, it's easy to see if I have something or not, easy to play.

After much hand-wringing I decided to split soundtracks between single artist and various (mixes). This solved the questions such as was "Rush" a soundtrack or an Eric Clapton album? or what about "Purple Rain" (Prince) or "This is It" (Michael Jackson) or "When Harry Met Sally" (Harry Connick, Jr.)?

As you say, the Artist division has a folder for each artist, then album. The Various division has a folder for each compilation or qualifying soundtrack. Sorry, no classical. Used to have a Christmas division, but that now follows the single artist vs various rule just like soundtracks.

Quite personal and leads to ease of retrieval.

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Even Microsoft’s NTFS supports hard links and symbolic links, but they are a mess to maintain.