A quick link to Apache Axis, the Java implementation of the SOAP protocol. I have been using this quite intensively in the last few weeks to create SOAP services to the Ensembl data.
Ensembl provides an interface to all the data of the Human Genome Project. In the underlying database all the mapping information for genes, exons, introns, etc. is stored. One of the projects I am involved in at work is to build pipelines for additional mapping information.
SOAP seems to be working very well to integrate Java and Perl based information sources together. I am not so sure if it usable for high throughput pipelines.