The solution used in the 3D6B editor approaches this problem by trying to change the internal representation of the software away from 3d surfaces to something that is closer to pen and paper. With this approach, we try to get rid of the internal representation of the computer: rather, what the user inputs, what the computer stores internally, and what the rendering engine renders are all the same thing. This removes the discontinuities of the process and approaches the process possible with pen and paper.
Since pen and paper are available everywhere, one design principle in the 3D6B project was to get it as easily accessible as possible. Since internet-equipped computers are available everywhere, we made this a web service, where the 3D6B editor is a Java applet. For places with no internet connection, the editor can be used in an application mode, where the connection to the web database is replaced by file operations.
This also meant that no special hardware should be required. In practice however, sketching with mouse is much more difficult than with a pen-based interface, so the editor is easiest to use with a drawing tablet.