My software preference is iThoughtsHD on the iPad, mainly because I find it easy to use and is set-up to email back the result in several forms, including as an image and as a text outline. It is structured and visual, which I can show the student(s) straight away when talking through my comments.
Why bother? Again a personal view but the visual structuring of the information I find helpful to me both when I am producing the map and the afterwards when I check progress. One of the other reasons, again a personal view, it is fairly enjoyable to do, and to look at afterwards. I find myself more likely/willing to view these afterwards than when I make written comments normally.