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?This is pretty much what I'm used to do, too.
I want to stress that using multiple event sheets is a key for organization, even more than using functions and groups. While the latter might steal some ms, event sheets are merged to one big event sheet on export (if I recall correctly), so basically there is no disadvantage in using them. Oh, and the comment option is there: Use it, everywhere, anytime.
I often thought: "Bah, that's a too easy solution for the problem. Don't need to make notices."
And just 2 days later I thought: "How the heck does this work, what did I do here?"
In general, it is all just about visual organization. The less text at once, the easier for us to follow. Imagine the book "The lord of the rings" without being seperated into parts, chapters, sections, breaks and indentation. Would anyone have read it?