I added MSMQ to my WCF web service (which was running OK) by adding the following endpoint to the service in web.config file

<endpoint
    address="net.msmq://server/private/queue1"
    binding="netMsmqBinding"
    bindingConfiguration="MsmqConfiguration"
    contract="ITestQueue" />

I also added the following binding

<netMsmqBinding>
    <binding name="MsmqConfiguration"
       exactlyOnce="false">
       <security mode="None"/>
    </binding>
</netMsmqBinding>

Once I deployed the Wcf service on Windows Server 2008, I also enable net.msmq on the website using the following command

appcmd set app "localhost/service" /enabledProtocols:net.msmq

However when I try to point to the svc file from my browser I got an Error 503 instead. Removing the MSMQ endpoint and I have the service up and running again.

After that I have a look at the website via the IIS Management Console and I realize that http protocol is not enabled for the website anymore

A normal web app will have http protocol such as below

At last I figure out that the appcmd actually overwrote the settings instead of adding on to it. So the correct appcmd command is:-

appcmd set app "localhost/service" /enabledProtocols:net.msmq, http

And I have the site running again with both http and msmq protocol enabled.