Hawk Sugano shows how he tracks his todos, notes and idea with indexcards.
With that many indexcards (4,000 of them) in 7 months, it must be working!
Go to his gallery at flickr and take a look. It opens my eye with the level of his organization. It takes the indexcard usage to the next level.
Also take a look at his Indexcarding System manual on his implementation and methods of using indexcard and why did he choose analog than digital.
Maximizing Productivity [Hawk Sugano @ Flickr]