I need to create 5 methods on the server side, which will work with binary data. The remote clients are applet and JavaScript. The Client will send files to the server, and
Depending on your container version, Jersey (or any other JAX-RS implementation) will still use a Servlet for dispatching requests to the appropriate handler.
If your application is truly RESTful, then JAX-RS will do what you want. Otherwise, consider using a FrontController to interpret the Request and forward it to the appropriate handler.
Also, don't confuse XML or JSON with REST. You will get these for free in most (if not all) JAX-RS implementations, but these implementations still delegate content marshalling to other libraries (e.g. JAXB).