I keep my index cards in chronological order : the newest card comes at front of the card box. All cards are clasified into four kinds and tagged according to the contents. The sequence is equivalent to my cultural genetic code.
Although it may look chaotic at the beginning, it will become more regulated soon. Don't be afraid to sweep out your mind and capture them all. Make visible what is going on in your brain. Look for a pattern behind our life.
Ref. : @blog, Chronological Order in the Dock