How to manage extensive notes?

I use a combination of tools:

• for timelines, I use Aeon Timeline.
  It's a paid software but it works well and there are developments still being wrought which should make it even better.

• for organising ideas, networks, processes, hierarchies and confusing relationships between characters, I use yEd (freeware).

• for organising family trees and large bodies of people which connect either by blood or not throughout several generations, I use Gramps (freeware; powerful genealogy software).

• for creating maps (of countries, cities, streets, houses... even scenes, to keep track of who is where), I use CC3
  It's a paid bunch of software products. Worthwhile if you need to visualise what you're writing.

• for organising notes in almost a wiki-like fashion and bring together all my info and notes (including images exported from the previous software programmes), I use Realm Works.
  It's a software programme and online service mostly directed at RPG players, but I've been using it to keep my novels (historical fiction, with a crazy amount of people, plots, locations, specific objects, maps, terminology... all the while having to keep track of what is attestedly historical, likely historical, long time legend and my own decisions). I don't know how I'd manage without it.

It's also easy to import word and pdf stuff into this huge database, which allows for linking anything you wish and establish relationships between characters. One weak point is that you can't print anything out of it just yet, but it's a work in process. They'll get there.

For me, I love folders. I can't get enough of em. I would create a folder titled WritingProjects, and then within create a folder called FanFiction. Within there, what ever the overall project name you want for your individual project. Within those project folders you can create separate folders such as World building, Characters, Plot, what ever note categories you may have for this specific project.

This would now allow you to more easily go to the desired notes without having to sift through 20 documents of world building to get to the 1 you need for character. You can just go right to the character. Even better, you can have multiple instances of file explorer open so that you can have all 3 folders open at once and just switch to the folder you need. As you work through the story, you can combine documents, even delete documents as they are no longer needed. Maybe even create a new folder for documents that are no longer needed but instead of deleting it and losing those notes, you have them archived just in case you realized, you actually did need something still.

Ultimately, I personally love folders. You know that when you open up the world building folder, everything in there will be related to world building. Of course, if you need to further sub categorize, you can create folders as needed. Say within world building you have a folder for environment, one for culture, one for animals/plants and so on. Just depends on how organized/OCD you want to get with it.

I will be honest, this might seem like a hassle to some with having so many folders to go in and out of, but this is how my brain works the best when it comes to organizing. I compartmentalize everything down to pretty specific categories.

Everyone else has thrown in their two bits, so I'm going to try mine.

I completely understand the problem of too much notes (currently I have over fifty documents detailing different notes and like three pages of the fic itself. World-building/exploring before narrative, but I digress) and I have to agree with ggiaquin that folders will help with this quite a bit.

However, one thing that I consider to be my saving grace in the almost year of note building that I have completed, is having a single master reference document. This document lists off all of your other docs in a Bullet List fashion. The bullets can show your folders and your documents so you know what documents are where and what each of them entail. Here's an example from my Master doc (I omitted the contents of the Picture References folders because that's a lot of bullets):

Also, like shown in the picture. Google docs helps keep everything in one place and you can access it anywhere (also, much less fallible than a USB).