Those jobs are most likely asking that you have experience with one or more of the major app server vendors, i.e. WebLogic, WebSphere, or JBoss. It's a bit different from what you're used to with servlets & JDBC, but it's still just Java. Typically you have to deal with things like JNDI lookups, dependency injection, messaging queues, maintaining application state between transactions, object/relational mapping, etc.
I have found that for most J2EE projects, it's more about knowing how components and systems are configured and how they work together than it is about any specific programming skill. And you also spend a lot more time waiting for the server to start up ;);