When you create web service "MyService" using IDE (JAX-WS 2.0), you get class
like this:

@WebService
public class MyService {
}

If you deploy it to Tomcat, your service will be named "MyService". If you move
it to GlassFish, it will be named "MyServiceService". (IMHO it's a bit strange -
isn't it regulated by JAX-WS spec? perhaps no). It makes your service less
portable and is rather undesirable, I think. 
The simplest solution is to change it to:

@WebService(serviceName="MyService")
public class MyService {
}

In such a case it will be always named "MyService".

So I think it would be better if NetBeans by default generated web service
classes with serviceName annotation, preventing from unpleasent surprises during
deployment.