There are many ways of deploying Mule ESB into a production environment. According to the documentation, it appears that running Mule as a standalone service is the recommended way of doing so.
Are there any reasons for NOT running Mule standalone in production? I'm sure its stable, but how does it compare to Tomcat as far as performance, reliability, and resource utilization go?
Should I still consider running it within Tomcat for any reason?
Using Tomcat, or any other web container, allows you to use the web tier of that container for HTTP inbound endpoint (via the Servlet transport) instead of either Mule's HTTP or Jetty transports.
Other differences are found in class loading, handling of hot redeployment and logging.
Now the main reason why people do not use Mule standalone is corporate policy, ie "thou shalt deploy on _". When production teams have gained experience babysitting a particular Java app/web server, they want you to deploy your Mule project in that context so they can administer/monitor it in a well-known and consistent manner.
But if you're happy with the inbound HTTP layer you get in Mule standalone and you are allowed to deploy it in production, then go for it. It's production ready.