The best idea processing toolkit

When an interesting problem strikes us, a flash of thoughts and various concerns floods into our mind and they turn into vague visuals. To convert them into real world stuff, we have to begin with concrete models. The importance of a note taking application at this point is very crucial, we need to draw models, we need to sketch arrows, we need to sketch workflows, we need to write appropriate descriptions.

And it is a crucial point for productivity, it is also important that how much importance you give at this stage to your ideas, this has something to do the amount of respect you give to your own thoughts.
So doing a computer application which can do it wisely is a NP hard problem, because I think for this pre-alpha stage of thoughts nothing is better than a pen and a paper. The best thought processing toolkit is a pan and paper, no application can disrupt it.