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
Can't vouch for it, but red5 is an open source flash server written in Java, which claims support for streaming mp4 and has implementations of mp4 IO objects which may be able to create said format.
Also, IBM created their Toolkit For MPEG-4 a while back and though it's not free, it might help.