There's no multi module archetype for JavaEE6 that I know of, yet. I planned on making one, but can't give an ETA.
However, you can start by looking at http://code.google.com/p/open-archetypes/
I suggest you create the project based on multi-javaee5-archetype first, then :
- update the version to 6 in the maven-ear-plugin configuration of the ear project
- update the version to 3.1 in the maven-ejb-plugin of the ejb project
- use a web.xml v3.0 in the web project or maybe add a new module to the base project, based off the jboss EE6 archetype, then add it as a dependency of the ear project
Note that app clients are not supported yet in m2e-wtp (it's almost ready though, so should be soon in m2e-wtp's dev builds)