What's the difference between standalone and domain on JEE6?

That's not really correct. Standalone is fine for production. It's commonly used in production, especially when you only need one instance of the server.

Domain is used when you run several instances of JBoss AS and you want a single point where you can control configuration from. You can read more about it in the documentation.

Update

The link has been changed to the latest version of WildFly as the JBoss AS 7 documentation has been archived, but is still available at https://docs.jboss.org/author/display/AS71/Admin%20Guide.html#8094211_AdminGuide-StandaloneServer

Standalone mode

• each JBoss server has its own configuration
• single JVM process

Domain mode

• central control of multiple servers
• central configuration for multiple servers

It's important to understand that the choice between a managed domain and standalone servers is all about how your servers are managed, not what capabilities they have to service end user requests. This distinction is particularly important when it comes to high availability clusters.

So, given all that:

• A single server installation gains nothing from running in a managed domain, so running a standalone server is a better choice.
• For multi-server production environments, the choice of running a managed domain versus standalone servers comes down to whether the user wants to use the centralized management capabilities a managed domain provides.
• Running a standalone server is better suited for most development scenarios. Any individual server configuration that can be achieved in a managed domain can also be achieved in a standalone server, so even if the application being developed will eventually run in production on a managed domain installation, much (probably most) development can be done using a standalone server.

For the Above explanation and more follow this link