Java framework and gui to convert several file format between them (iRex irx, Aiptek walltop, jarnal jaj, jetbook color scribble, svg and more).
You can see a video tutorial of how to convert (for example) Jetbook Color scribble in Jarnal and, using it, how to generate a new PDF merging original document and your handwritten notes:

Part 1 - using Jetbook Color to sketch PDF document
http://www.youtube.com/watch?v=-ffIFNO0rNw

Part 2 - using jCrossSketch v.0.6 to convert previous notes in Jarnal and to generate a new PDF
http://www.youtube.com/watch?v=McEs3c0N6Iw