One of the most usefule tools I've come across for any project that requires planning is ClockingIt. Clocking it acts as your one stop shop for file storage, milestone and asset tracking, and even personal management. It gives you access to chatrooms and forums (QA, anyone?), and gives you user by user control over who has access to what areas when. I'm only just now getting into the planning phase for my platformer, but I'm definately going to be using ClockingIT from start to finish. It's an invaluable tool, and best of all... IT'S FREE!
I've worked on several indie projects in my efforts to make my break into the industry, and the one thing that I've seen consistantly is a lack of planning. "Hey, we'll just make this!". I think that's because of the media misconception that game design is the same as sitting on your butt playing XBox all day, when it's actually a lot of hard work. If it's something you love, then it won't FEEL like hard work, but if it's not a true passion then it will be just like any other crappy job, except with worse hours.
When working in an indie environment, it's easy to think that you can just "make" the game. Well, I'll just do some graphics here and some programming there and Voila! A game! But it's not like that at all! The first thing is to set up a road map. One of the other designers I worked with refused to write anything down. I'd ask for an asset list, or anything to help me work on art for the game and he'd say "Uhm... do these two characters and then we'll figure out the rest." But it was always the same two characters.
I spent _hours_ working on a GDD for him, and a story. So I sent it to him, "Uh... yeah, that's fine." "Do you see anything that won't work?" "Nah, it's fine. Can we do art now?" Of course, that lead to issues down the road when - lo and behold - something in my rough draft of a GDD didn't pan out. To which his answer was always, "Oh well, we'll just scrap it and make another one." Needless to say, this game went nowhere. Working without at LEAST a general GDD is like driving someplace knew without directions. You might eventually get there, but you'll have wasted so much time it might not even matter.
Anyway, all of this to say, make yourself a roadmap. Know your desitnation so that you can figure out how to get where you're going. Once you've got that, dive in head first. What order or on what timeline you do things is negotiable when you're an Indie, but at least KNOW what you need to DO!
More ramblings soon!