I would like to find a FREE MP4 (container) writer for Java. I do not need an encoder, only something which can write the correct atoms given their expected values. Bonus
I have implemented a QuickTimeWriter class which can write a QuickTime container in pure Java.
As far as I know, the QuickTime file format is structurally equivalent to MPEG-4 Part 14. There are only a few minor differences in the fields inside atoms/boxes.
So, with an MPEG-4 spec on your lap, and a few hours of work, you should be good.