Scratching over lines to put emphasis on them is going to be a waste of time in motion.
Since the mind map is a clock work approach you could use the different coloured pens to signify different emphasis. Red core concept, Blue sub heads, main ideas relating to the core concept, black for further branches and green for by - lines. Along with nice symbols you have a workable option for using ordinary pens. In anycase good mind maps can be done with just one colour. Later review you can put in markers of different colours to group ideas (drawing shapes around the complete 'heading and it's branches).
Have a look at felt tip writing pens of the style used for overhead projectors when you angle them some more you get a bit more play on their lines. The come from the faber Castell range and are actually required in some schools over pens.
You could also look at a small good quality set of coloured pencils. I've managed to create some interesting mind maps with pencils even though they are not going to scan that well they do serve the purpose for notes.
I've used gel pens to as well as the humble blue or black pen to create something a drunk spider would be proud of. It serves the purpose. I just glance at the words and connecting lines and I have a trigger for remembering the notes so looks isn't everything. Being involved with the process is a good chunk of the work.
Alex
