Chris Adamson wrote a great article on manipulating QuickTime files using Java APIs. The article goes in depth on how to read the QuickTime file structure with Java and similarly how to write out QuickTime files. Also, there's mention that MPEG-4 is roughly QuickTime based so the same techniques can apply for what looks like might be the winning next generation multimedia document format. Apparently MPEG-4 has hooks to program interactivity through Java.
Adamson also points to an Apple tutorial on QuickTime, which helps in interpreting the structure and varied leaf nodes of a QuickTime file.
Memo to self: there's at least one popular multimedia file format that MochaTime could target