Well, several things.
1) If you're willing to route whatever special protocol you want to use in to an HTTP packet, then you can simply write a servlet and be done with it. You can readily shove pretty much any data you want down an HTTP request. If the efficiency of the protocol isn't an issue, it saves a lot of work and plumbing.
2) You can create a Java Resource Adapter using the Java Connector Architecture. These can do whatever you want, including listening to sockets, and the component will be delpoyed in the EJB container. But you get to write all of the plumbing yourself, for good or ill.
3) Which security issues disqualify Webservices? You can use HTTPS for transport encryption, and you can encrypt the messages themselves for when the messages go over an open network.
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