To be able to encode mp3 files with Sound Juicer on Ubuntu Jaunty Jackalope just install the package gstreamer0.10-plugins-ugly-multiverse.
If you then open sound juicer, in the preferences->output format->edit profiles you can now see the CD Quality, mp3 option.
The first time I ran it, the output format didn't had the mp3 option. I just edited the mp3 profile and tick two times the active checkbox.
Don't know if this is really necessary but now everything works. :D