If you have a WCF service exposing endpoints with the NetMsmqBinding, you may come across my old pal, error code 0xc00e002f when you have web application clients. If you’ve already had your required interactive login on the web server with your AppPool’s service account and have already registered your AppPool service account’s user certificate for message queuing, then you should be ok.
If you are using IIS 7 or 7.5, there is one more piece to the puzzle. Go into Advanced Settings on your Application Pool, and find “Load User Profile” under the Process Model section. “Load User Profile” on these latest versions of IIS needs to be true to get your service account’s user certificate passed to MSMQ. I fought this for a while before finally finding it. And now? 🙂