As Jim said, a socket connection is probably the best way to handle communications to your GCE instance.
However - depending on your communications needs - you could go a lot of different ways. For instance, you could have your GCE machine periodically poll a page on your App Engine site. Another alternative is to communicate over XMPP: the PHP GAE runtime doesn't have access to the XMPP service, but you could write a Java/Python module and use the App Engine XMPP capability.