That's a tough question, and one I"m still working on. At first I used index cards, which worked a bit but were very time consuming - at times I was spending more time filling out the cards than I was actually writing. It also felt artificial, as I was filling them out thinking, OK, what's his favorite color, his favorite song? What is the chidhood trauma that he's hiding, and all the other questions you're supposed to ask yourself to "Know Your Character".
I made a major card for each character of the book: even those that just popped in for several lines. I used them for a bit to remember eye color and everything else that I could potetially mix up later on.
What happened, character wise, was that over time and drafts I built, and rebuilt, the characters in my head. They went from being outlines to being real people. At that point my index cards were no longer needed.
Then I started having plotting issues, and used post-its (Julie Cohen's course on that at York is amazing). That system helps me switch chapters around, see where things are getting long, and if the key moments aren't too clumped together.
For geography (fantasy writer here) I made myself a bunch of maps. I can't draw worth beans but I love my little maps.
On top of index cards (no longer used), Post-its, and maps, I'm a great believer of notebooks, in which I keep track of everything: ideas, changes I've made, things to add, things to remove, and a daily writing diary (a sentence or two, telling myself what the day's aims are). I have one notebook per project, to keep ideas seperate.
I keep telling myself that I should to use Scrivner as a means of keeping all my ideas in one place, but I (deeply) fear the Scrivner learning curve. If anyone has good ressources for learning Scrivner in a jiffy, please don't hesitate to send them my way. ;-)
In the end, I think you'll find as many types of organisation as there are writers.