After having trouble finding much better than ODE wrappers for 3D physics in Java, someone pointed me this week to JBullet. Seems to work great from my experiments so far (just learning how to run the demos from a new Eclipse project at this point).
Pure Java is nice.
Side note, a project to convert x86 to JVM bytecode and automatically run DLL and ELF so files would be sweet. That would auto-port lots of native libraries to Java. Well, in some cases you might need semi-deep OS emulation.