In our last test, Windows Vista finally had a win with its Java stack. The j2dbench performance was significantly better on Windows Vista Premium, but that's likely attributed to the Intel graphics stack on Linux having little in the way of performance optimizations. Mesa isn't yet performance oriented and there is no kernel memory manager or other features found in Ubuntu 8.10 for Intel graphics. This though should improve vastly with time considering the invasive work currently taking place within the X.Org / Mesa community and the eventual adoption of the Gallium3D architecture.
Well, Java on Ubuntu was pretty much the hands-down winner compared to Microsoft Windows Vista Premium SP1. Running the Java tests on Ubuntu had experienced significant advantages when it came to file encryption, Fast Fourier Transforms, Successive Over Relaxation, Monte Carlo, and the composite Java SciMark performance. In only the Sunflow test were the results between Ubuntu and Windows even close. With the Java 2D Microbenchmark, Windows was faster but that likely falls on the Intel Linux graphics driver having little in the way of performance optimizations and Java on Linux not yet utilizing the X Render extension.
Comparing Sun's Java and OpenJDK / IcedTea on Ubuntu had roughly the same performance between the two except for a few areas (FFT and Monte Carlo) where the official JVM was noticeably faster.
These six tests didn't stress all areas of the Java stack, but it provides a brief look at where the Java performance is between Ubuntu Linux and Windows Vista. Also keep in mind that we were using the stock packages available by default in each operating system, which had very slight differences between them. To share your thoughts on Java, stop by the Phoronix Forums.