mp4 is just a container. To join the videos inside, I assume they are probably h264/AVC, they have to be the same resolution (and codec of course) and you should be able to join them just fine.
edit: oh yea, the audio should be the same format too
edit2: you might want to use a GUI, Yamb, it's listed on the mp4box page. otherwise i think the commands for joining files is
MP4Box -cat file1.mp4 -cat file2.mp4 output.mp4