Sitting at a computer changes the way you think. You need to know when to walk away from the computer and when to come back.
I think mind mapping software is a bad idea. Mind maps are supposed to capture free associations. But the very act of sitting down at a computer puts you in an analytical frame of mind. In other words, mind mapping is a right-brain activity, but sitting at a computer encourages left-brain thinking. Mind mapping software might be a good way to digitize a map after you’ve created it on paper, but I don’t think it’s a good way to create a map.
When I need to sort out projects and priorities, I do it on paper. After that I may type up the results. I like to capture ideas on paper or on my voice recorder but then store them online.
When I do math, I scribble on paper, then type up my results in LaTeX. Scribbling helps me generate ideas; LaTeX helps me find errors. I’ve found that fairly short cycles of scribbling and typing work best for me, a few cycles a day.
In the past, we did a lot of things on paper because we had no choice. Today we do a lot of things on computers today just because we can. It’s going to take a while to sift through the new options and decide which ones are worthwhile and which are not.
Daniel Pink’s book A Whole New Mind has a good discussion of left-brain versus right-brain thinking. As he points out, the specialization between the left and right hemispheres of the brain is more complicated than once thought. However, the terms “left-brain” and “right-brain” are still useful metaphors even if they’re not precise neuroscience.
Also, to read more on how computers influence our thinking, see Andy Hunt’s book Pragmatic Thinking and Learning.