Finally I found a good video editing library to use with Java.
To me it seems very well written and documented. There are a number of useful examples. The API is very clean and compact: you can write a transcoder in very few lines of code. See the Media Tool introduction on http://wiki.xuggle.com/MediaTool_Introduction to have an idea.
Precompiled binaries are available for MacOSX 10.7+, Win 32/64 and Linux.
BTW: I’m using precompiled library version 5.4 on MacOSX 10.6.8 and it works just fine