Other than pencil & paper? I found freemind, the mapping tool very useful. Any other ideas?
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8A whiteboard and a camera to capture what's on the whiteboard quickly, to be able to move on to the next thing.
Post-It notes
Whiteboard and decent coloured pens
Walls to pin the notes on to
Digital camera to capture all the work
The book Domain Driven Design :)
In all seriousness, when other people are involved, a whiteboard. Later Microsoft Visio to formalize the drawings from the discussion. A former Design Director for a competitor who now works for our company routinely captures an audio recording of conferences - he uses it for his own benefit; he doesn't use it to call people out.
I find this (FreeMind) an excellent way to capture structured unstructured thoughts. Great for brainstorming, although it doesnt cover the diagram side.
Personally I like physical paper notebooks and pencils to workout ideas :-), but some times I use FreeMind.
Check this list of Mind Mapping Software.
Usualy we use writeboard. Personaly - pencil & paper. And one of most comfortable tools what I'm using for taking notes, making todo and other lists is VIM Outliner. If you don't use VIM, I believe you can find any other comfortable outliner.
Mind mapping is really useful for this purposes. When you have distributed team, you may wan to use web-based mind mapping applications. I'm using Mindomo to share initial (and not only) requirements documentation with the rest of requirements management and development team.
Also I quite often use draw&scan approach to capture and share ideas, comments, schemes, etc. Often it works much better than writing a plain e-mail or doc.