We recently migrated an application from a Weblogic 7.x server to a 9.x server. In earlier versions of Weblogic, deciding where to put JMS objects like queues and topics was easy -- you just put them on a JMS server.
Weblogic 9.x adds an extension to the JMS spec. You can either deploy JMS objects to a "system module" or an "application module." According to the documentation, the main difference between the two is ownership. System modules are owned by the Weblogic administrator, while application modules are owned by the Weblogic developers. The administrator has limited ability to modify application modules.
You can package application modules with your application in an .ear file. System modules are deployed more traditionally, using the administration console or the Weblogic Scripting Tool.
We are both administrators and developers on our Weblogic box, so the question of control is not a criterion in our decision. We use Glassfish, and sometimes ActiveMQ, in our dev environment, so I'm a little reluctant to pick application modules, as they are a Weblogic extension to the JMS spec. I must admit, however, that the idea of packages topics and queues in an ear file is very appealing.
What thought process did your team go through when picking between system and application JMS modules?