Just for fun, I tried to run a FFT program from the IBM Ninja (Numerically Intensive Java) package. After implementing a few more native methods, it ran, but to my surprise it ran about as fast as under JDK 1.4 (with Sun's Hotspot VM). Not bad for totally unoptimized code
The cfft.java source that I ran can be viewed here, the resulting executable (in a zip) can be found here and I've updated the project snapshot. For the array package, follow the Ninja link.