Great question... probably something every game designer needs to think about.
I use a notebook most of the time. Track what I'm doing, write down where I left off, sketch ideas, etc... one notebook per project and crapton of pencils, just in case.
Within C2, I use a lot of groups and comments. It takes some extra work, but if you're diligent, C2 isn't too tough to organize. I've found a love for Functions in regard to organization. Break up tasks into widgets that can be called or altered without having too re-write larger pieces of game logic. Never be afraid to use multiple event sheets, either--all variables on one, all sub-functions on another (organized into groups), and several others for different layers or mechanics.
I guess there's no one method, huh?