I've taken a butt-ton of notes this past year, and just for the one story. I've recently begun organizing them using a free trial of Scrivener, just to see if I like it (still too soon to give my honest opinion yet, sorry!). Before then, though, I've just been using good old Google Docs to organize.
Also the free notes app on my smartphone to jot down the sudden idea spurts right away. I also have the Google Docs app for updating when I'm away from the computer, or in bed and too lazy/tired to get up.
In the Notes app, I organize stuff bullet style, and alphabetically (Character Notes, Character Quotes, Plot Points, Random Ideas, Revisions, etc....). In Google, I have entirely separate docs for world-building terminology, story outlines, and more extensive character pages, among other stuff.
Much of my older stuff is hand-written, though, and I have yet to switch them all over to digital 
Honestly, I wouldn't stress too much about organizing every. Single. Note. Sometimes it's good enough that you got that stuff down in the first place. And honestly, the next thing you write or type is bound to be an improvement (I leaf through my older notes and go whaaat was I thinking?).
But I do still recommend Google Docs, it's done wonders for me. And it's FREE! And other folks here seem to be in agreement.