Moro :)
What come to the pure Java world, it depends. There are way too many+1 Web Service projects. Eclipse contains some tools as well, but I've neve used them. Instead of Eclipse tools, I've used more or less Open Source software, mainly Apache Axis and Spring Web Services, but that's J2EE world.
The good news is that Domino's Web Service engine is based on the same AXIS WS engine. And actually it is quite good and easy to use. Just create one Java Interface class (or implementation class I think) and you are good to go to publish the WSDL. Standards rules :)
What did you mean by the Java tools available only in XPages?