In general, it is possible to get Aware IM to work with any J2EE compliant application server, such as Web Sphere. In fact, early versions of Aware IM used to support Weblogic server out-of-the-box. Then we decided to stick with the open source versions of application servers, so that we can package the entire system in one installation.
To integrate with WebSphere you need to modify Aware IM startup parameters specified in the AwareIM/BIN/BASServer.props file. You need to specify WebSphere specific settings for JMS and JNDI. Have a look at this file and if you are an expert in Java technologies you will know what to do. Mind you, though, that we have never tested Aware IM with WebSphere, so some unexpected surprises are possible. We can overcome those together provided that there is enough incentive for us to do so.
I am not sure, though, why you need to integrate Aware IM with WebSphere and why you can't run JBoss in parallel with WebSphere.
IIS is not a J2EE compliant server, so Aware IM will not work directly with it. But just like WebSphere and JBoss they can co-exist happily on the same machine!