There're quite some. Here's a short list as a result of some googling:
- jffmpeg (an extension of JMF, last release in Jan 2006)
- FMJ and FFMPEG-Java (aka. Freedom for Media in Java, a more up-to-date alternative of JMF/jffmpeg, last release in Sep 2007)
- Xuggler (yet another Java lib for FFMPEG , last release in Feb 2010)
- JAVE (Java Audio Video Encoder, last release in Apr 2009)
From the number of Google hits it's hard to decide which one is the most popular. It looks as if people would be generally unsatisfied with JMF+jffmpeg (it's not keeping up with ffmpeg's evolution) and they turn to FMJ as a solution. Based on the downloadable releases FMJ seems to be heavily out-of-date as well. Although it's current CVS version might be usable. Xuggler seems to be the most up-to-date of them all, but it's last release is a year old too.
I'm quite disappointed in all these projects, obviously there's nothing fancy that "just works".
Of course there's also the option to call the ffmpeg commandline directly, but it requires you to figure out all the necessary ffmpeg options for the tasks you wish to accomplish.