Keeping my ideas organized has nothing to do with the fact that I'm a writer by the way, by profession, this is something that everyone should do.
I find that being organized adds a lot of value and impact in the long run, and there are a number of ways I keep mine in check:
1- I have a big board in my room that is full of markings and future plans. No matter how silly you think the idea is, always write it down. Chances are, in the future you'll come to a point eventually when you are stuck and need ideas (where this will be perfect. You can mash up a couple of ideas that fit and flesh your story out more).
2- I have a mini-fridge (worst investment I have ever made by the way) that I use for this as well, I use magnets to hang one-page outlines on it. Create a challenge for yourself, create as many one page outlines as you can, or you can write your goals or ideas for future scenes in your novel/story. Hanging them will give you the urge to finish them just so you can feel the rush of taking one out. Food, and beverages won't hurt too.
3- I have the "Book of Secrets" which is a notebook that I always keep close to me, and write all ideas, tips, and observations regarding anything I encounter in it. Someone once said "if you write it, you don't have to remember it" which is the perfect excuse to do this (for the lazy ones). You'll always encounter challenges, or be taught lessons whether its from YouTube videos (yes Jenna Moreci, we're looking at you) or random lists on the internet. Even quotes on Twitter too (#amWriting #writerTips).
4- I keep a separate document for large projects that is basically a 'cheat sheet'. For Dragon Tooth, I have "Dragon Tooth: World Information" which lists all the guilds and characters in the story. Having a one place go to like this will definitely keep you in track or how the story is going. This will help tremendously when you take those long breaks (which we all know you take).
5- Outline, outline, and outline! Outline your entire story, novel, book or script. Anything that needs writing, needs outlining. It makes you focused and determined to finish because you know how it ends basically. One will never understand the importance of this step unless they start writing a novel of around 70K words and they lost track of the events that took place previously and have to re-re-re-read the entire thing again just to ensure there are not plot holes.
These are my top five methods of how to organize my writing. Always remember: it's better to write it, than to remember it.
This is all for now, if you have any questions, remember you can drop me a line anytime and I would be more than happy to assist you.