Seeing as my post has had a few viewings and no replies I thought I would actually post an update myself.
In the end (last year) I decided that I had 2 options. 1 was to use environment variables which can be set in the properties-service.xml file (or passed as command line parameters in the start script when the jvm is invoked). The other was to edit the web xml in the deployer. Look in the deployers/jbossweb.deployer folder and you will see a web.xml. It is possible to add parameters here that will be picked up by the deployed application.