This complements an earlier question on usable, fast C++ matrix libraries. I've looked at the Java Matrix Benchmark, and it seems like the performance of java matrix libraries is all over the place. The Apache Commons Math library seems like a simple solution, but I'm curious for others recommendations. Specifically, I'm curious which libraries are much easier/more performant than the others, and/or if Java library writers are better off just using JNI to call to an existing, better developed native matrix libraries. (Though that seems like it could make the code less portable or more of a hassle to setup.) 
Recommendations for a usable, fast Java matrix library?
linear algebra;software
In general, you are almost always better off using the JNI if you are concerned about performance.  A JNI interface to a fast BLAS is implemented by the Intel Math Kernel Library, which would be option if you are considering a cross-platform commercial offering.  If you are looking for a fast open source offering, you might want to consider jblas, which tries to be multi-platform (with a few holes), and wraps ATLAS, a reasonably fast open source implementations of the BLAS.Your mileage will vary based on the specific matrix operations you are performing and how big the matrices are.Related Questions:Parallel Scientific Computation Software Development Language? - A discussion of comparisons and considerations for using Java against other programming languages. 