If you want real interoperability, you'll have to stick to those data types listed in the WS-I specification (i.e. integers, strings, etc.).
However, as long as your Java web service is configured to serialize your custom Java object into the outgoing
SOAP message properly (with a custom serializer in Axis-speak), the .NET client can be programmed to parse that SOAP message and construct a similar (but not the same, of course) object from that XML.