@ Lazzaro: yes I know, thanks for specifying, but the problem is that
the duration of audio and video files I record don't match each other.
You can try to grab a rectangle of your desktop with recordmydesktop
(from commandline) it accept also a jack connection for audio data so,
if your system dont crash, you can record what you see and what you hear
in your perceptive time.
The output is a theora file rather compressed but usable. I was able to
make this series of videos : http://vimeo.com/5708413
but considering the size of your project then this could also be a
useless answer :)