I have a Java client that consumes SharePoint 2010 standard web services (sitedata.asmx, permissions.asmx, etc) written with JAX-WS implementation from the JDK 6.
So
You have to disable the tranparent authentication in java. you can do this either by dropping in a custom rt.jar or using reflection to modify the java classes.
tryTransparentNTLMServer and tryTransparentNTLMProxy are the fields in the HttpURLConnection which you need to set accessible and then to false when using the reflection method. Obviously just change this class if your making your own rt.jar