See the WebSphere 5.1 InfoCenter at http://www-306.ibm.com/software/webservers/appserv/was/library/library51.html
Without knowing your application structure and configuration it is difficult to determine the cause of your specific problem. You say that your home page displays, but that no other links are accessible, "as the webserver is not communicating with the Application server." Who served your home page then, the web server or the WebSphere HTTP transport? If you are you specifying a port number, other than 80, in your URL (e.g. http://localhost
:9080/home.jsp), then the WebSphere internal HTTP server served the page, unless you added * 80 to the default virtual host. Did you install the plugin when you installed WebSphere and IHS? Did you regenerate the plug-in after installing your new application? If you didn't, the web server will not know about your new application.
Look at the following log files in for clues: <WAS_HOME>/logs/server1 (assuming that is your server name). Specifically, look at SystemOut.log, SystemErr.log. If the plugin is working, there likely will be a file named http_plugin.log in <WAS_HOME>/logs, as well. IHS also has a logs directory, so look in there as well.
Finally, look at <IHS_HOME>/conf/httpd.conf. At the end of the configuration file you should have a LoadModule entry that points to the plugin module, and a WebSpherePluginConfig entry that points to the plugin configuration file (plugin-cfg.xml). Look at this file and make sure there is a Uri name= entry in UriGroup for your application.