I use MindManager (although other mind mapping software is available) all the time. I find it incredibly useful for noting my ideas and attaching links, documents, etc., into those ideas as they expand. I currently have 14 business ideas on the go, two of which I am taking forward now and, hopefully, the rest in the future. There is no way I could manage them all without this type of software.
Before I take on a non-trivial task (programming or otherwise) I just write down a few ad-hoc examples on paper and make notes of special cases, concerns or questions I need answered.
I don't buy into the more organized attempts to get me to adopt any specific scheme.