The thing that differentiates Tomcat from the "full stack"
J2EE and JEE servers is that Tomcat only implements the
servlet and
JSP parts of the Enterprise Java specs. It does that very well - products such as
JBoss actually embed a copy of Tomcat in themselves to handle
their servlet and JSP needs - but that's all it does. Tomcat has no JMS capabilities.
Fortunately, there are libraries that can be incorporated into web applications that will be running under Tomcat. Several of them, in fact. Apache and ObjectWeb both have messaging libraries that I know of, and I think without too much trouble you can find around a half a dozen libraries to choose from.