JAX-WS: Addresses advanced QoS requirements that commonly occur in enterprise computing. When compared to JAX-RS, JAX-WS makes it easier to support the WS-* set of protocols, which provide standards for security and reliability, among other things, and interoperate with other WS-* conforming clients and servers.

JAX-RS: Makes it easier to write web applications that apply some or all of the constraints of the REST style to induce desirable properties in the application, such as loose coupling (evolving the server is easier without breaking existing clients), scalability (start small and grow), and architectural simplicity (use off-the-shelf components, such as proxies or HTTP routers). You would choose to use JAX-RS for your web application because it is easier for many types of clients to consume RESTful web services while enabling the server side to evolve and scale. Clients can choose to consume some or all aspects of the service and mash it up with other web-based services.