I have heard that this is what JavaRebel does but is there any other good way to deploy a new version of an EAR while allowing users to remain active on the previous version? We use JBoss for the application server...
Hot Deploy a Java EAR to Minimize or Eliminate Downtime of an Application on a Server?
Vladimir's suggestion around using a load balancer is a pretty sure way of achieving what you want. Keep in mind, it need not necessarily be a high-end hardware load balancer. Rather, if you front your JBoss server with a native web server (Apache or IIS) and mod_jk or mod_proxy, you can maintain one common web facade and implement the applicable loading and routing routines at EAR upgrade time.
As I understand WebLogic has a feature called parallel deployment to eliminate downtime during EAR version upgrade. You can deploy the new version without stopping the existing application and once the new version deployed successfully you can switch over transparently from the old one to new one.
I am not sure if other application server supports this.