Creating templates isn't something we've really nailed down yet as we're still trying to figure out if developers really just want a way to publish their WAR files using their own app/build templates. We recently added maven support, which provides a more standard mechanism for starting projects and then using Stax as a deploy target. If you're interested in doing your own template, I've got a copy of the stax-basic app template up in GitHub that you can use as a reference.
Thanks for the shout out to Stax on your blog. Glad to hear your JPublish framework was easy to get running.
I noticed on your blog that you use Heroku for your Rails apps. Please let us know about any features from Heroku's Rails platform you'd like to see for your Java apps on our platform.