I’ve been using XMind http://www.xmind.net/ to try to keep my ideas and task organized. The free version is fine for a single developer but apparently you can link in other people and brain storm together.
I’ve just found that it’s really useful for laying out my task and marking which ones rely on which others. I can then tag them with icons to show how far done each task is. It’s also quite useful for brainstorming. Just type an idea and then as your mind branches off into various ideas you can easily build those branches while tracking your ideas.
I have no relationship with the company, I just think it’s a really useful tool.