Migrating from WebLogic to Tomcat is a tricky thing, since WebLogic is a full-stack J2EE server and Tomcat isn't. There are likely to be all sorts of things that people were used to relying on that aren't in Tomcat.
JMS, of course, is a big example. And unless WebLogic's JMS ConnectionFactory is explicitly guaranteed to operate as a stand-alone component in Tomcat, it's extremely unlikely that you can excerpt it from WebLogic and expect it to run in Tomcat. And that's not counting the legal issues, since you'd still have to be in good standing with Oracle to do so - you can't just "borrow" it.
Assuming you can't use WebLogic JMS, however, there are component libraries that add JMS support to Tomcat. I think there's an Apache/jakarta JMS implementation. And unless my memory fails me, the ObjectWeb group has a JMS package called "James". Others probably exist as well. Plus, you can simply use JBoss, which, being a full-stack J2EE implementation has its own JMS subsystem in the container (probably Apache's). JBoss uses an embedded copy of Tomcat as its servlet/JSP container. ObjectWeb uses a similar strategy in its JOnAS server.
An IDE is no substitute for an Intelligent Developer.