I'm about to start the first real phase of my game development which will consist of the acquisition of information, resources and the definition of where I want to go and what I will need for that. I just want to make sure that I'm prepared as best as possible before I actually start development.

I don't like the thought of using Microsoft Word or Excel for my project management... I already worked with MS Project but I don't think it fits my needs.

I need a software where I can easily maintain project steps, milestones, important issues, information about technologies and engines I use, as well as simple notes and thoughts I just want to write down.

I usually prefer a whiteboard for stuff like that but unfortunately it's not a persistent way of storing. ;) Also writing it down the old-school way is something I can think of, but only for quick notes...

Which software do you use for that?
Are there commonly used programs?
Is there any free software at all?