i don’t know what kind of files are used to generate itunes/winAmp animations, but i’m pretty sure you can’t create those things with Max, nor interact with those.
You surely can create animations from sound datas, though, in Max, especially with Jitter. basically you have spectroscope~ … but anyway i don’t think Max as the most common way to make such things.
Interacting with java animations should not be a problem since there is a max api for java, Max supports Java, but as for Flash, i sincerely doubt it.