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Business logic in java websocket endpoint/JAX-RS?

What's the best practices for implementing business logic in a web-application that uses a Websocket connection? specifically, how to use a Java websocket endpoint effectively to implement services and functionalities of the system?
Does the websocket endpoint replace Java web-services (JAX-RS) functionality entirely?

WebSocket is not a replacement for JAX-RS.
Both technologies have their usecases; if I were you, I would do my research before asking questions like this one.
The first question is about the business logic - and that always depends. You can adapt in some way MVC patter when dealing with JAX-RS, since there is a tight connection between Http Request and Response and you can even use some templating engine to process your output (Jersey - JAX-RS RI - contains pre-built support for this scenario). WebSocket is very different in terms of data processing, there is one "persistent" TCP connection which you can use to transmit messages from/to either side, which usually requires different programming model and typical usecase would include sending/receiving short status update messages to some interactive front-end (javascript) application.

Which common communication protocol to use for communicating with a java layer in a web architecuture

I am planning to design such an architecture for my website as shown in picture above. I am building a core platform in Java that do the communication with DB and other high processing tasks and modules can hook up with the core by means of defined interfaces.
Modules could be anything like, front-end website, email box, admin consoles etc. and could be built on any technology like PHP, Java, ruby on rails etc.
Now tell me which communication protocol should I use for communication between modules and core. Protocol must be something that majority of languages understand and can be process easily in both way communication.
And if somebody find any flaws with such an architecture then kindly suggest a better one that provide great extensibility and flexibility.

I would use HTTP, exposing a REST API on the Core, such as Thilo suggested.
The complexity lies on the trade-offs between RPC (procedural model) of traditional webservices, and the Resource Model, which fits better when using http requests (verbs GET, POST, PUT and DELETE on URI's, complemented with some headers and a body).
Yet, this makes a soft, easy to maitain and portable ditribution. Every single client module may be built on a whole different technology, which allows you to use "the best tool for the job".
Not to mention HTTP advantages for caching, rewriting, load-balancing, ssl, etc.

So basically this is a SOA-like architekture. JavaEE and EJB (3+) or the Spring frameworks come to mind immediately.
The components (your "modules") are usually coupled via SOAP services with an optional Enterprise Service Bus (ESB) between frontend, backend and the composite services.
Whether this is a good match for your case or simply oversized... noone but you can say...

Web Services vs Messaging

What kind of arguments one should use when choosing between integration using web service vs JMS? I'm familiar with basics of both approaches however in some cases it is unclear as to which one would be the best for a given situation. I guess I'm looking for a high overview comparison with use cases.
thanks

JMS is a messaging service. It is asynchronous and 2 directional, i.e. you can write application that both sends and receives messages. But this must be application implemented typically in java. I mean it cannot be thin client. And standard protocol of JMS is TCP based, so it may be blocked by firewall.
Web service is designed as a transport over HTTP, so it typically passes firewalls. But it is one directional: client calls server; server cannot call client. It just can response client's calls. Client of web service (especially RestFull web service) is very simple, so it can be easily implemented as a thin client (e.g. AJAX client).

Good question.
I will use Web Service when:
1. Dealing with cross domains, typically services environment when I am not sure about the client technology.
2. Need Synchronous response.
And pickup Messaging when (Hope you mean Messaging not just Java version):
1. Need Asynchronous request/response.
2. High Availability.
3. Confirmed Delivery.

C++ JMS client or C++/C SOAP Client

I have an application in C++, but it'll need to 'talk' to Java based message-service. In the past we used WebSphere MQ and used their C++ libraries to do the 'talking'.
So I am in search of (ideally) free C++ to Java solution which doesn't hold the whole JVM in memory.
The other option I've looked into is SOAP.
I've looked into Axis2-C but it gives me the whole server implementation, which I don't need.
I've seen talk about gSOAP but saw mixed comments here. And again it seems to be providing me with a whole server.
I could write the code myself - but it goes against my (Java based) belief that excellent free code exists out there.
Thanks!
A'z

There are a couple of points here which don't make sense to me, JMS is a java specific abstraction over a generic messaging API, much the same way that JDBC is a java specific abstraction over a generic database API.
I can't imagine anyone wanting a JDBC driver for a C++ application, they would rather use an ODBC driver.
So if I assume that your objective is to send messages without using Websphere MQ from a C++ application, then I can recommend that you consider the following:
Do you need asynchronous messaging? i.e. store message on queue until message is consumed?
If yes, then web-services will not work for your application, unless you are prepared to host a web-server to receive the responses, and call back to your application.
You haven't mentioned whether the underlying java based message service is going to be JMS or WebServices.
You could consider using ActiveMQ as a messaging provider, it provides an implementation of the JMS API and also implements the STOMP protocol, which has client libraries for a number of languages including C++.
You could leave open your decision for end-point protocols while you try out various options, by implementing an integration layer using something like Mule.
You can quickly develop small integrations on Mule e.g. to accept a Message on ActiveMQ, and post it to a WebService and put the WebService response on a different ActiveMQ response queue. Or vice-versa, accept web-service call and post SOAP onto JMS queue, wait for JMS response and build SOAP response.
There are many ESB-like frameworks which can facilitate these sort of integrations to various degrees :
Mule
ServiceMix
Fuse
Apache Camel
Spring Integration
JBoss ESB
EDIT:
Given the clarification I will refine my answer:
You need a common message broker that is accessible to C++ and Java such as ActiveMQ.
You need a small / lightweight integration layer such as some of those above to accept from ActiveMQ and forward to SonicMQ, and vice-versa.
2.1 From what I know of Sonic, they have an ESB stack that should be able to do this instead of using one of the containers/frameworks mentioned above, but that will open up issues of integration ownership between you and the client.
I found 3 links showing Sonic support for C and C++ :
- http://www.sonicsoftware.com/products/docs/sonicmq_app_server_ds.pdf
- http://www.sonicsoftware.com/developer/documentation/docs/sonicmq_c_v60.pdf
- http://communities.progress.com/pcom/servlet/JiveServlet/download/10809-3-10161/cclients_readme_76.htm (dodgy mime type on this link)

The SonicMQ site seems to indicate that they support C++.
It would appear that this is suitable.

There are C++ libraries for SonicMQ. The main constraint is that you have to be using the same build (ie. STL libraries, etc) that Sonic used to compile the libraries.
http://web.progress.com/en/sonic/sonicmq-clients.html
Of course you asked this question over half a year ago, so this information is probably a bit late. :-)

Best Java supported server/client protocol?

I'm in the process of writing a client/server application which should work message based. I would like re-use as much as possible instead of writing another implementation and curious what others are using.
Features the library should offer:
client and server side functionality
should work message based
support multi-threading
should work behind load balancer / firewalls
I did several tests with HTTPCore, but the bottom line is that one has to implement both client and server, only the transport layer would be covered. RMI is not an option either due to the network related requirements.
Any ideas are highly appreciated.
Details
My idea is to implement a client/server wrapper which handles the client communication (including user/password validation) and writes incoming requests to a JMS queue:
#1 User --> Wrapper (Check for user/password) --> JMS --> "Server"
#2 User polls Wrapper which polls JMS
Separate processes will handle the requests and can reply via wrapper to the clients. I'd like to use JMS because:
it handles persistence quite well
load balancing - it's easy to handle peaks by adding additional servers as consumer
JMSTimeToLive comes in handy too
Unfortunately I don't see a way to use JMS on it's own, because clients should only have access to their messages and the setup of different users on JMS side doesn't sound feasible either.

Well, HTTP is probably the best supported in terms of client and server code implementing it - but it may well be completely inappropriate based on your requirements. We'll need to actually see some requirements (or at least a vague idea of what the application is like) before we can really advise you properly.

RMI works nicely for us. There are limitations, such as not being able to call back to the client unless you can connect directly to that computer (does not work if client is behind a firewall). You can also easily wrap your communication in SSL or tunnel it over HTTP which can be wrapped in SSL.
If you do end up using this remember to always set the serial version of a class that is distributed to the client. You can set it to 1L when you create it, or if the client already has the class use serialver.exe to discover the existing class's serial. Otherwise as soon as you change or add a public method or variable compatibility with existing clients will break.
static final long serialVersionUID = 1L
EDIT: Each RMI request that comes into the server gets its own thread. You don't have to handle this yourself.
EDIT: I think some details were added later in the question. You can tunnel RMI over HTTP, then you could use a load balancer with it.
I've recently started playing with Hessian and it shows a lot of promise. It natively uses HTTP which makes it simpler than RMI over HTTP and it's a binary protocol which means it's faster than all the XML-based protocols. It's very easy to get Hessian going. I recently did this by embedding Jetty in our app, configuring the Hessian Servlet and making it implement our API interface. The great thing about Hessian is it's simplicity... nothing like JMS or RMI over HTTP. There are also libraries for Hessian in other languages.

I'd say the best-supported, if not best-implemented, client/server communications package for Java is Sun's RMI (Remote Method Invocation). It's included with the standard Java class library, and gets the job done, even if it's not the fastest option out there. And, of course, it's supported by Sun. I implemented a turn-based gaming framework with it several years ago, and it was quite stable.

It is difficult to make a suggestion based on the information given but possibly the use of TemporaryQueues e.g. dynamically created PTP destinations on a per client basis might fit the problem?
Here is a reasonable overview.

Did you tried RMI or CORBA? With both of them you can distribute your logic and create Sessions

Use Spring....Then pick and choose the protocol.

We're standardizing on Adobe's AMF as we're using Adobe Flex/AIR in the client-tier and Java6/Tomcat6/BlazeDS/Spring-Framework2.5/iBATIS2.3.4/ActiveMQ-JMS5.2 in our middle-tier stack (Oracle 10g back-end).
Because we're standardizing on Flex client-side development, AMF and BlazeDS (now better coupled to Spring thanks to Adobe and SpringSource cooperating on the integration), are the most efficient and convenient means we can employ to interact with the server-side.
We also heavily build on JMS messaging in the data center - BlazeDS enables us to bridge our Flex clients as JMS topic subscribers. That is extremely powerful and effective.
Our Flex .swf and Java .class code is bundled into the same .jar file for deployment. That way the correct version of the client code will be deployed to interact with the corresponding middle-tier java code that will process client service calls (or messaging operations). That has always been a bane of client-server computing - making sure the correct versions of the respective tiers are hooked up to each other. We've effectively solved that age-old problem with our particular approach to packaging and deployment.
All of our client-server interactions work over HTTP/HTTPS ports 80 and 443. Even the server-side messaging push we do with BlazeDS bridged to our ActiveMQ JMS message broker.