We have decided to have 5 different applications that could be plugged in and out from each-other, formed by at least three modules; ejbs, ejb clients and a gui.
I found developing an app. made up of different modules in Eclipse quite limiting. You can't configure different web.xml's or persistence.xml's for different configurations you have.
IDEA9 on the other hand, has just what I had in my mind. It has a great artifacts screen where you can control where what configuration will go, which modules compile-output will go where and what jars to copy on what directory.Things I missed from Eclipse were the subclipse and Propedit plugins. Also on IDEA the run screen strangely only had "deploy all" button. To deploy my apps. seperately I needed to use autodeploy feature or the remote server setting. IDEA9 has 30 days of free evaluation period where you can test it. For now we are still bound to Eclipse but we might choose to use IDEA in the future.
Another major change was since we needed an Application Server for ejbs we couldnt use the developer friendly Tomcat. I had a nice experience with GlassFishV3 server while doing the JEE6 projects, but our company would probably choose BEA's Weblogic. Every AS needs some twiks. Weblogic had some class loader problem with our app. which we needed to overcome by defining a weblogic-application.xml. Details could be found here. One last thing to note is, weblogic jndi look-upsi needs the qualified class names. Like if you have a mapped name of "my/MyService" you have to look it up with; "my/MyService#interfaceName..."
GUI part of our app. is made of jsf & spring. I have used the springs LocalStatelessSessionProxyFactoryBean to lookup EJB's. It does it's job but I believe it has some missing features. It would be far more efficient, while developing, if I didn't had to restart my gui after my ejb's were deployed. On that case instead of performing the lookup again spring just throws an exception, though I think I could find a solution that does that.
Thats what I do mostly here. I started getting bored with that... From now on I think I will mostly just hit people behind their neck to point them to right direction.