There is another Java implementation of Skein-512-512 by the H2 Database folks.
From their site:
This is a Java implementation of the Skein-512-512 hash algorithm. It is only about 250 lines of code, and compatible with the revised (version 1.1) test vectors and reference implementation.
I tried to optimize for speed, and get 130 MB/s on my laptop (a MacBook Pro, 2.53 GHz Intel Core 2 Duo; Java 1.6, server mode). I don't know how is that compared to the fully optimized version because I don't have a good C compiler.