I used index cards to plot out my most recent book and so enjoyed them that I'm using them again.
I carried my little box of index cards (not a real box, just the cardboard sleeve they came in) absolutely everywhere with me, and whenever I had any sort of thought about the book -- it went on a card.
Some of those were backstory ideas, some were about character, some were Exciting Things that should happen -- every idea, big or small, had a card. Sometimes I used the back of the card for more info about that idea (looking up interesting words, checking historical facts, creating family trees).
Then I would sort the ideas/cards into some sort of order.
I also had a notebook for this project, with, again, family trees and so forth -- and, most important, a page where I just had the chapters listed by number and by the main thing that would happen in each one.
Writing this book was a breeze! I loved slapping cards to the back of the deck as I wrote!
Anyway, it also helps me to have something I can spread out physically (on the floor, as others have said) and rearrange. AND -- I love not losing those little flashes of inspiration that come at odd moments.